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<h3>
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/148f00554b69f8cb921cf77fea094025597fa3a5">148f0055</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-24T16:42:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use https for links where available.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/fa3937381a74c9b3f7fbe708a329256ee4141ec2">fa393738</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-24T16:44:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix rather than disable broken test_cluster_sync
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/7d50f8d318478b6bb767b008c540da954f4fc92a">7d50f8d3</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-24T17:07:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">edit patch descriptions, include upstream status
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#cf10603a1c12bbbc3e45d0711e954076cdb8820f">
debian/patches/0009-skip-test-without-google-cloud-sdk.patch
</a>
</li>
<li class="file-stats">
<a href="#31abb991f60e62441a34137fbf2a74ea3c4d1ea7">
<span class="new-file">
+
debian/patches/bug322_cluster_sync.patch
</span>
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</li>
<li class="file-stats">
<a href="#7af1b47e7c28e029594f4457cc27d4671dc7fd42">
<span class="new-file">
+
debian/patches/link_security.patch
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#260fb267aa59c740952b443e87e306a192a8d82e">
debian/patches/workaround_sphinx_issue.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,8 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Rebecca N. Palmer ]</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Use Python 3 in subprocess calls.</span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> * Disable buggy test (upstream 322) and tests needing conda or docker.</span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Fix buggy test (upstream 322).</span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Disable tests needing conda or docker.</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Delete unused patches.</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Use boto3 (like upstream) not boto.</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Reproducibility: don't ship (timestamped) test logs.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,6 +21,7 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> * Update dependencies, add minimal-Depends test.</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Privacy: use local dagre-d3, add missing Javascript dependencies,</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> don't appear to show live status when we don't.</span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Use https for links where available.</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Thu, 09 Apr 2020 14:57:00 +0100</span>
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<li id="cf10603a1c12bbbc3e45d0711e954076cdb8820f">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#cf10603a1c12bbbc3e45d0711e954076cdb8820f"><strong>debian/patches/0009-skip-test-without-google-cloud-sdk.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: chrysn <chrysn@fsfe.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Date: Mon, 11 Dec 2017 16:15:05 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Subject: Skip tests with that depend on google-cloud-sdk if not installed</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Skip tests that depend on google-cloud-sdk if not installed</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">There is no package in Debian that provides the required module, and its</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">absence makes the test fail.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">This is not currently in Debian - see RFP #759578.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: chrysn <chrysn@fsfe.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">Whether this needs a Debian RFP or should be forwarded is undecided yet given</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">the author has no clue about what those Google Cloud SDK actually does.</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">--- a/tests/test_remote_gs/Snakefile</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_remote_gs/Snakefile</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -1,15 +1,19 @@</span></span>
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<li id="31abb991f60e62441a34137fbf2a74ea3c4d1ea7">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#31abb991f60e62441a34137fbf2a74ea3c4d1ea7"><strong>debian/patches/bug322_cluster_sync.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Allow running tests in parallel</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug: https://github.com/snakemake/snakemake/issues/322</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: accepted https://github.com/snakemake/snakemake/pull/326</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/tests/tests.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -244,6 +244,7 @@</span> def test_remote():</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> def test_cluster_sync():</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.environ["TESTVAR"] = "test"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> run(dpath("test14"), snakefile="Snakefile.nonstandard", cluster_sync="./qsub")</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span></pre>
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<li id="7af1b47e7c28e029594f4457cc27d4671dc7fd42">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#7af1b47e7c28e029594f4457cc27d4671dc7fd42"><strong>debian/patches/link_security.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Change links to HTTPS where available</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: accepted https://github.com/snakemake/snakemake/pull/325</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">diff --git a/docs/executing/cluster-cloud.rst b/docs/executing/cluster-cloud.rst</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">index 9bb1a8b3..988ad2fe 100644</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/executing/cluster-cloud.rst</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/executing/cluster-cloud.rst</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -236,7 +236,7 @@</span> and forward it to the cluster scheduler:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> $ snakemake --cluster "qsub --runtime {params.runtime}"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-If your cluster system supports `DRMAA <http://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+If your cluster system supports `DRMAA <https://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> E.g. jobs can be cancelled upon pressing ``Ctrl+C``, which is not possible with the generic ``--cluster`` support.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> With DRMAA, no ``qsub`` command needs to be provided, but system specific arguments can still be given as a string, e.g.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/executing/interoperability.rst b/docs/executing/interoperability.rst</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/executing/interoperability.rst</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/executing/interoperability.rst</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -9,7 +9,7 @@</span> Interoperability</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> CWL export</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ----------</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Snakemake workflows can be exported to `CWL <http://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Snakemake workflows can be exported to `CWL <https://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> Since, CWL is less powerful for expressing workflows than Snakemake (most importantly Snakemake offers more flexible scatter-gather patterns, since full Python can be used), export works such that every Snakemake job is encoded into a single step in the CWL workflow.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> Moreover, every step of that workflow calls Snakemake again to execute the job. The latter enables advanced Snakemake features like scripts, benchmarks and remote files to work inside CWL.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> So, when exporting keep in mind that the resulting CWL file can become huge, depending on the number of jobs in your workflow.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/index.rst b/docs/index.rst</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gh" style="color: #999;">index 164f6a3e..a448f1f0 100644</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/index.rst</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/index.rst</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -113,7 +113,7 @@</span> Support</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> Citation</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> --------</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> See :doc:`Citations <project_info/citations>` for more information.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -154,41 +154,41 @@</span> Please consider to add your own.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> * Goormaghtigh et al. 2018. `Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells <https://mbio.asm.org/content/mbio/9/3/e00640-18.full.pdf>`_. mBio.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> * Ramirez et al. 2018. `Detecting macroecological patterns in bacterial communities across independent studies of global soils <https://www.nature.com/articles/s41564-017-0062-x>`_. Nature microbiology.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> * Amato et al. 2018. `Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes <https://www.nature.com/articles/s41396-018-0175-0>`_. The ISME journal.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <http://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <http://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <https://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <https://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> * Beatty et al. 2017. `Giardia duodenalis induces pathogenic dysbiosis of human intestinal microbiota biofilms <https://www.ncbi.nlm.nih.gov/pubmed/28237889>`_. International Journal for Parasitology.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> * Meyer et al. 2017. `Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400397/>`_. Molecular Biology and Evolution.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <http://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <https://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> * Beisser et al. 2017. `Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes <https://peerj.com/articles/2832/>`_. PeerJ.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> * Piro et al 2017. `MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling <https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0318-y>`_. Microbiome.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> * Dimitrov et al 2017. `Successive DNA extractions improve characterization of soil microbial communities <https://peerj.com/articles/2915/>`_. PeerJ.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <http://www.pnas.org/content/114/5/1105.short>`_. PNAS.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <http://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <https://www.pnas.org/content/114/5/1105.short>`_. PNAS.</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <https://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> * Etournay et al. 2016. `TissueMiner: a multiscale analysis toolkit to quantify how cellular processes create tissue dynamics <https://elifesciences.org/content/5/e14334>`_. eLife Sciences.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <http://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.</span></span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <https://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <https://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.</span></span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> * Li et al. 2015. `Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6>`_. Genome Biology.</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <http://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.</span></span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <http://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <http://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.</span></span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <http://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <http://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <http://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.</span></span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <https://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <https://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <https://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <https://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <https://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.</span></span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <https://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> * Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <https://biologydirect.biomedcentral.com/articles/10.1186/s13062-015-0071-8>`_. Biology Direct.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <http://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.</span></span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.</span></span>
</pre>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <http://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <http://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <http://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <https://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <https://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <https://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <https://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.</span></span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> * Köster et al. 2014. `Massively parallel read mapping on GPUs with the q-group index and PEANUT <https://peerj.com/articles/606/>`_. PeerJ.</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <http://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <http://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <http://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.</span></span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <http://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.</span></span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <http://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <http://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <http://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.</span></span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <https://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <https://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <https://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <https://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <https://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <https://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <https://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> .. toctree::</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/project_info/citations.rst b/docs/project_info/citations.rst</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gh" style="color: #999;">index a21b7344..07d2f5a4 100644</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/project_info/citations.rst</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/project_info/citations.rst</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span> When using Snakemake for a publication, **please cite the following article** in</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> Cite This</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> =========</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> More References</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -26,11 +26,11 @@</span> More References</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> Another publication describing more of Snakemake internals:</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <http://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <https://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> And my PhD thesis which describes all algorithmic details:</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <http://hdl.handle.net/2003/33940>`_</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <https://hdl.handle.net/2003/33940>`_</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> Project Pages</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -48,4 +48,4 @@</span> The markdown syntax is</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> [](https://snakemake.readthedocs.io)</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> Replace the ``3.5.2`` with the minimum required Snakemake version.</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-You can also `change the style <http://shields.io/#styles>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+You can also `change the style <https://shields.io/#styles>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/project_info/faq.rst b/docs/project_info/faq.rst</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gh" style="color: #999;">index e1ef4d2a..d80010d9 100644</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/project_info/faq.rst</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/project_info/faq.rst</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="p">@@ -188,7 +188,7 @@</span> and have in the Snakefile some Python code that reads this environment variable,</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> I get a NameError with my shell command. Are braces unsupported?</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> ----------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-You can use the entire Python `format minilanguage <http://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+You can use the entire Python `format minilanguage <https://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> This:</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -315,7 +315,7 @@</span> On unix, you can make use of the commonly pre-installed `mail` command:</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> snakemake 2> snakemake.log</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> mail -s "snakemake finished" youremail@provider.com < snakemake.log</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <http://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <https://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> I want to pass variables between rules. Is that possible?</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> ---------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/project_info/more_resources.rst b/docs/project_info/more_resources.rst</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gh" style="color: #999;">index b62d1fa1..dd0783ec 100644</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/project_info/more_resources.rst</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/project_info/more_resources.rst</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="p">@@ -14,8 +14,8 @@</span> Talks and Posters</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> * `Invited talk by Johannes Köster at the Broad Institute, Boston 2015. <https://slides.com/johanneskoester/snakemake-broad-2015>`_</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> * `Introduction to Snakemake. Tutorial Slides presented by Johannes Köster at the GCB 2015, Dortmund, Germany. <https://slides.com/johanneskoester/deck-1>`_</span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> * `Invited talk by Johannes Köster at the DTL Focus Meeting: "NGS Production Pipelines", Dutch Techcentre for Life Sciences, Utrecht 2014. <https://speakerdeck.com/johanneskoester/workflow-management-with-snakemake>`_</span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `Taming Snakemake by Jeremy Leipzig, Bioinformatics software developer at Children's Hospital of Philadelphia, 2014. <http://de.slideshare.net/jermdemo/taming-snakemake>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `"Snakemake makes ... snakes?" - An Introduction by Marcel Martin from SciLifeLab, Stockholm 2015 <http://marcelm.net/talks/2015/snakemake>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `Taming Snakemake by Jeremy Leipzig, Bioinformatics software developer at Children's Hospital of Philadelphia, 2014. <https://de.slideshare.net/jermdemo/taming-snakemake>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `"Snakemake makes ... snakes?" - An Introduction by Marcel Martin from SciLifeLab, Stockholm 2015 <https://marcelm.net/talks/2015/snakemake>`_</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> * `"Workflow Management with Snakemake" by Johannes Köster, 2015. Held at the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute <https://speakerdeck.com/johanneskoester/workflow-management-with-snakemake-1>`_</span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="p">@@ -27,14 +27,14 @@</span> External Resources</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> These resources are not part of the official documentation.</span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `A number of tutorials on the subject "Tools for reproducible research" <http://nbis-reproducible-research.readthedocs.io>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `A number of tutorials on the subject "Tools for reproducible research" <https://nbis-reproducible-research.readthedocs.io>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> * `Snakemake workflow used for the Kallisto paper <https://github.com/pachterlab/kallisto_paper_analysis>`_</span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `An alternative tutorial for Snakemake <http://slowkow.com/notes/snakemake-tutorial/>`_</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `An alternative tutorial for Snakemake <https://slowkow.com/notes/snakemake-tutorial/>`_</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> * `An Emacs mode for Snakemake <http://melpa.milkbox.net/#/snakemake-mode>`_</span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> * `Flexible bioinformatics pipelines with Snakemake <http://watson.nci.nih.gov/~sdavis/blog/flexible_bioinformatics_pipelines_with_snakemake/>`_</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> * `Sandwiches with Snakemake <https://github.com/leipzig/SandwichesWithSnakemake>`_</span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `A visualization of the past years of Snakemake development <http://youtu.be/bq3vXrWw1yk>`_</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `A visualization of the past years of Snakemake development <https://youtu.be/bq3vXrWw1yk>`_</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> * `Japanese version of the Snakemake tutorial <https://github.com/joemphilips/Translate_Snakemake_Tutorial>`_</span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* `Basic <http://bioinfo-fr.net/snakemake-pour-les-nuls>`_ and `advanced <http://bioinfo-fr.net/snakemake-aller-plus-loin-avec-la-parallelisation>`_ french Snakemake tutorial.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* `Basic <https://bioinfo-fr.net/snakemake-pour-les-nuls>`_ and `advanced <https://bioinfo-fr.net/snakemake-aller-plus-loin-avec-la-parallelisation>`_ french Snakemake tutorial.</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> * `Mini tutorial on Snakemake and Bioconda <https://github.com/dlaehnemann/TutMinicondaSnakemake>`_</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> * `Snakeparse: a utility to expose Snakemake workflow configuation via a command line interface <https://github.com/nh13/snakeparse>`_</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/snakefiles/configuration.rst b/docs/snakefiles/configuration.rst</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/snakefiles/configuration.rst</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/snakefiles/configuration.rst</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="p">@@ -64,7 +64,7 @@</span> With the `Pandas library <https://pandas.pydata.org/>`_ such data can be read an</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> samples = pd.read_table("samples.tsv").set_index("samples", drop=False)</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> reads in a table ``samples.tsv`` in TSV format and makes every record accessible by the sample name.</span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-For details, see the `Pandas documentation <http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html?highlight=read_table#pandas-read-table>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+For details, see the `Pandas documentation <https://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_table.html?highlight=read_table#pandas-read-table>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> A fully working real-world example containing both types of configuration can be found `here <https://github.com/snakemake-workflows/rna-seq-star-deseq2>`_.</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> ---------------------</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="p">@@ -104,7 +104,7 @@</span> Instead, for data provenance and reproducibility reasons, you are required to pa</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> Validation</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> ----------</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-With Snakemake 5.1, it is possible to validate both types of configuration via `JSON schemas <http://json-schema.org>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+With Snakemake 5.1, it is possible to validate both types of configuration via `JSON schemas <https://json-schema.org>`_.</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> The function ``snakemake.utils.validate`` takes a loaded configuration (a config dictionary or a Pandas data frame) and validates it with a given JSON schema.</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> Thereby, the schema can be provided in JSON or YAML format. Also, by using the defaults property it is possible to populate entries with default values. See `jsonschema FAQ on setting default values <https://python-jsonschema.readthedocs.io/en/latest/faq/>`_ for details.</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> In case of the data frame, the schema should model the record that is expected in each row of the data frame.</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span> the schema for validating the samples data frame looks like this:</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> .. code-block:: yaml</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $schema: "http://json-schema.org/draft-06/schema#"</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $schema: "https://json-schema.org/draft-06/schema#"</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> description: an entry in the sample sheet</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> properties:</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> sample:</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/snakefiles/deployment.rst b/docs/snakefiles/deployment.rst</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gh" style="color: #999;">index 775a3ff8..4fa0fc93 100644</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/snakefiles/deployment.rst</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/snakefiles/deployment.rst</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="p">@@ -61,8 +61,8 @@</span> Integrated Package Management</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> -----------------------------</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> With Snakemake 3.9.0 it is possible to define isolated software environments per rule.</span>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Upon execution of a workflow, the `Conda package manager <http://conda.pydata.org>`_ is used to obtain and deploy the defined software packages in the specified versions. Packages will be installed into your working directory, without requiring any admin/root priviledges.</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Given that conda is available on your system (see `Miniconda <http://conda.pydata.org/miniconda.html>`_), to use the Conda integration, add the ``--use-conda`` flag to your workflow execution command, e.g. ``snakemake --cores 8 --use-conda``.</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Upon execution of a workflow, the `Conda package manager <https://conda.pydata.org>`_ is used to obtain and deploy the defined software packages in the specified versions. Packages will be installed into your working directory, without requiring any admin/root priviledges.</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Given that conda is available on your system (see `Miniconda <https://conda.pydata.org/miniconda.html>`_), to use the Conda integration, add the ``--use-conda`` flag to your workflow execution command, e.g. ``snakemake --cores 8 --use-conda``.</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> When ``--use-conda`` is activated, Snakemake will automatically create software environments for any used wrapper (see :ref:`snakefiles-wrappers`).</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> Further, you can manually define environments via the ``conda`` directive, e.g.:</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/snakefiles/modularization.rst b/docs/snakefiles/modularization.rst</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/snakefiles/modularization.rst</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/snakefiles/modularization.rst</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="p">@@ -52,7 +52,7 @@</span> The `Snakemake Wrapper Repository`_ is meant as a collaborative project and pull</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> Common-Workflow-Language (CWL) support</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> --------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-With Snakemake 4.8.0, it is possible to refer to `CWL <http://www.commonwl.org/>`_ tool definitions in rules instead of specifying a wrapper or a plain shell command.</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+With Snakemake 4.8.0, it is possible to refer to `CWL <https://www.commonwl.org/>`_ tool definitions in rules instead of specifying a wrapper or a plain shell command.</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> A CWL tool definition can be used as follows.</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> .. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="p">@@ -75,7 +75,7 @@</span> Snakemake will execute the rule by invoking `cwltool`, which has to be available</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> When using in combination with :ref:`--use-singularity <singularity>`, Snakemake will instruct `cwltool` to execute the command via Singularity in user space.</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> Otherwise, `cwltool` will in most cases use a Docker container, which requires Docker to be set up properly.</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-The advantage is that predefined tools available via any `repository of CWL tool definitions <http://www.commonwl.org/#Repositories_of_CWL_Tools_and_Workflows>`_ can be used in any supporting workflow management system.</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The advantage is that predefined tools available via any `repository of CWL tool definitions <https://www.commonwl.org/#Repositories_of_CWL_Tools_and_Workflows>`_ can be used in any supporting workflow management system.</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> In contrast to a :ref:`Snakemake wrapper <snakefiles-wrappers>`, CWL tool definitions are in general not suited to alter the behavior of a tool, e.g., by normalizing output names or special input handling.</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> As you can see in comparison to the analog :ref:`wrapper declaration <snakefiles-wrappers>` above, the rule becomes slightly more verbose, because input, output, and params have to be dispatched to the specific expectations of the CWL tool definition.</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/snakefiles/remote_files.rst b/docs/snakefiles/remote_files.rst</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gh" style="color: #999;">index ca46f900..6915103c 100644</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/snakefiles/remote_files.rst</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/snakefiles/remote_files.rst</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span> Amazon Simple Storage Service (S3)</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> This section describes usage of the S3 RemoteProvider, and also provides an intro to remote files and their usage.</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-It is important to note that you must have credentials (``access_key_id`` and ``secret_access_key``) which permit read/write access. If a file only serves as input to a Snakemake rule, read access is sufficient. You may specify credentials as environment variables or in the file ``=/.aws/credentials``, prefixed with ``AWS_*``, as with a standard `boto config <http://boto.readthedocs.org/en/latest/boto_config_tut.html>`_. Credentials may also be explicitly listed in the ``Snakefile``, as shown below:</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+It is important to note that you must have credentials (``access_key_id`` and ``secret_access_key``) which permit read/write access. If a file only serves as input to a Snakemake rule, read access is sufficient. You may specify credentials as environment variables or in the file ``=/.aws/credentials``, prefixed with ``AWS_*``, as with a standard `boto config <https://boto.readthedocs.org/en/latest/boto_config_tut.html>`_. Credentials may also be explicitly listed in the ``Snakefile``, as shown below:</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> For the Amazon S3 and Google Cloud Storage providers, the sub-directory used must be the bucket name.</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="p">@@ -264,7 +264,7 @@</span> Web addresses must be specified without protocol, so if your URI looks like this</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> .. code-block:: text</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http://server3.example.com/path/to/myfile.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ https://server3.example.com/path/to/myfile.tar.gz</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> The URI used in the ``Snakefile`` must look like this:</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/snakefiles/rules.rst b/docs/snakefiles/rules.rst</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gh" style="color: #999;">index 04ddbe31..99fec6f5 100644</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/snakefiles/rules.rst</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/snakefiles/rules.rst</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span> Most importantly, a rule can consist of a name (the name is optional and can be</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> output: "path/to/outputfile", "path/to/another/outputfile"</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> shell: "somecommand {input} {output}"</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Inside the shell command, all local and global variables, especially input and output files can be accessed via their names in the `python format minilanguage <http://docs.python.org/py3k/library/string.html#formatspec>`_. Here input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. ``path/to/inputfile path/to/other/inputfile``).</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Inside the shell command, all local and global variables, especially input and output files can be accessed via their names in the `python format minilanguage <https://docs.python.org/py3k/library/string.html#formatspec>`_. Here input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. ``path/to/inputfile path/to/other/inputfile``).</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> From Snakemake 3.8.0 on, adding the special formatting instruction ``:q`` (e.g. ``"somecommand {input:q} {output:q}")``) will let Snakemake quote each of the list or tuple elements that contains whitespace.</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> Instead of a shell command, a rule can run some python code to generate the output:</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span> Finally, you can also define global wildcard constraints that apply for all rule</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> rule b:</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> ...</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-See the `Python documentation on regular expressions <http://docs.python.org/py3k/library/re.html>`_ for detailed information on regular expression syntax.</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+See the `Python documentation on regular expressions <https://docs.python.org/py3k/library/re.html>`_ for detailed information on regular expression syntax.</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> Aggregation</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="p">@@ -486,7 +486,7 @@</span> Inside the script, you have access to an object ``snakemake`` that provides acce</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> Apart from Python scripts, this mechanism also allows you to integrate R_ and R Markdown_ scripts with Snakemake, e.g.</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> .. _R: https://www.r-project.org</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Markdown: http://rmarkdown.rstudio.com</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Markdown: https://rmarkdown.rstudio.com</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> .. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/additional_features.rst b/docs/tutorial/additional_features.rst</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gh" style="color: #999;">index 54d1178e..af3973c7 100644</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/additional_features.rst</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/additional_features.rst</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="p">@@ -6,32 +6,32 @@</span> Additional features</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> .. _Snakemake: https://snakemake.readthedocs.io</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> .. _Snakemake homepage: https://snakemake.readthedocs.io</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> .. _GNU Make: https://www.gnu.org/software/make</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Python: http://www.python.org</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Python: https://www.python.org</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> .. _BWA: http://bio-bwa.sourceforge.net</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _SAMtools: http://www.htslib.org</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _BCFtools: http://www.htslib.org</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Pandas: http://pandas.pydata.org</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Miniconda: http://conda.pydata.org/miniconda.html</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Conda: http://conda.pydata.org</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _SAMtools: https://www.htslib.org</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _BCFtools: https://www.htslib.org</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Pandas: https://pandas.pydata.org</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Miniconda: https://conda.pydata.org/miniconda.html</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Conda: https://conda.pydata.org</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> .. _Atom: https://atom.io</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> .. _rpy2: https://rpy2.github.io</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> .. _R: https://www.r-project.org</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> .. _Docutils: https://docutils.sourceforge.io</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _slides: http://slides.com/johanneskoester/deck-1</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _slides: https://slides.com/johanneskoester/deck-1</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> In the following, we introduce some features that are beyond the scope of above example workflow.</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> For details and even more features, see :ref:`user_manual-writing_snakefiles`, :ref:`project_info-faq` and the command line help (``snakemake --help``).</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="p">@@ -144,7 +144,7 @@</span> When Snakemake is executed with</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> it will automatically create required environments and</span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> activate them before a job is executed.</span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-It is best practice to specify at least the `major and minor version <http://semver.org/>`_ of any packages</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+It is best practice to specify at least the `major and minor version <https://semver.org/>`_ of any packages</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> in the environment definition. Specifying environments per rule in this way has two</span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> advantages.</span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> First, the workflow definition also documents all used software versions.</span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/advanced.rst b/docs/tutorial/advanced.rst</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gh" style="color: #999;">index f7ead578..03a91988 100644</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/advanced.rst</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/advanced.rst</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="p">@@ -6,32 +6,32 @@</span> Advanced: Decorating the example workflow</span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> .. _Snakemake: https://snakemake.readthedocs.io</span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> .. _Snakemake homepage: https://snakemake.readthedocs.io</span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> .. _GNU Make: https://www.gnu.org/software/make</span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Python: http://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Python: https://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> .. _BWA: http://bio-bwa.sourceforge.net</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _SAMtools: http://www.htslib.org</span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _BCFtools: http://www.htslib.org</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Pandas: http://pandas.pydata.org</span></span>
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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Miniconda: http://conda.pydata.org/miniconda.html</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Conda: http://conda.pydata.org</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _SAMtools: https://www.htslib.org</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _BCFtools: https://www.htslib.org</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Pandas: https://pandas.pydata.org</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Miniconda: https://conda.pydata.org/miniconda.html</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Conda: https://conda.pydata.org</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> .. _Atom: https://atom.io</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> .. _rpy2: https://rpy2.github.io</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> .. _R: https://www.r-project.org</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> .. _Docutils: https://docutils.sourceforge.io</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _slides: http://slides.com/johanneskoester/deck-1</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _slides: https://slides.com/johanneskoester/deck-1</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> Now that the basic concepts of Snakemake have been illustrated, we can introduce advanced topics.</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/basics.rst b/docs/tutorial/basics.rst</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gh" style="color: #999;">index cc1cfb45..fe97f775 100644</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/basics.rst</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/basics.rst</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="p">@@ -6,32 +6,32 @@</span> Basics: An example workflow</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> .. _Snakemake: https://snakemake.readthedocs.io</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> .. _Snakemake homepage: https://snakemake.readthedocs.io</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> .. _GNU Make: https://www.gnu.org/software/make</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Python: http://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Python: https://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> .. _BWA: http://bio-bwa.sourceforge.net</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _SAMtools: http://www.htslib.org</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _BCFtools: http://www.htslib.org</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Pandas: http://pandas.pydata.org</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Miniconda: http://conda.pydata.org/miniconda.html</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Conda: http://conda.pydata.org</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _SAMtools: https://www.htslib.org</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _BCFtools: https://www.htslib.org</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Pandas: https://pandas.pydata.org</span></span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Miniconda: https://conda.pydata.org/miniconda.html</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Conda: https://conda.pydata.org</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> .. _Atom: https://atom.io</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> .. _Anaconda: https://anaconda.org</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> .. _RestructuredText: https://docutils.sourceforge.io/docs/user/rst/quickstart.html</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> .. _data URI: https://developer.mozilla.org/en-US/docs/Web/HTTP/data_URIs</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _JSON: http://json.org</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _YAML: http://yaml.org</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _DRMAA: http://www.drmaa.org</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _JSON: https://json.org</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _YAML: https://yaml.org</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _DRMAA: https://www.drmaa.org</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> .. _rpy2: https://rpy2.github.io</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> .. _R: https://www.r-project.org</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> .. _Rscript: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> .. _Docutils: https://docutils.sourceforge.io</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _slides: http://slides.com/johanneskoester/deck-1</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _slides: https://slides.com/johanneskoester/deck-1</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> Please make sure that you have **activated** the environment we created before, and that you have an open terminal in the working directory you have created.</span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gh" style="color: #999;">index 32ff8ca3..a098bc28 100644</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/setup.rst</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/setup.rst</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> Setup</span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Snakemake: http://snakemake.readthedocs.io</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Snakemake homepage: http://snakemake.readthedocs.io</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Snakemake: https://snakemake.readthedocs.io</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Snakemake homepage: https://snakemake.readthedocs.io</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> .. _GNU Make: https://www.gnu.org/software/make</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Python: http://www.python.org</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Python: https://www.python.org</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> .. _BWA: http://bio-bwa.sourceforge.net</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _SAMtools: http://www.htslib.org</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _BCFtools: http://www.htslib.org</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Pandas: http://pandas.pydata.org</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Miniconda: http://conda.pydata.org/miniconda.html</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Conda: http://conda.pydata.org</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Bash: http://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _SAMtools: https://www.htslib.org</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _BCFtools: https://www.htslib.org</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Pandas: https://pandas.pydata.org</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Miniconda: https://conda.pydata.org/miniconda.html</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Conda: https://conda.pydata.org</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Bash: https://www.tldp.org/LDP/Bash-Beginners-Guide/html</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> .. _Atom: https://atom.io</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Graphviz: http://www.graphviz.org</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _PyYAML: http://pyyaml.org</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Graphviz: https://www.graphviz.org</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _PyYAML: https://pyyaml.org</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> .. _Docutils: https://docutils.sourceforge.io</span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> .. _Jinja2: https://jinja.palletsprojects.com</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> .. _NetworkX: https://networkx.github.io</span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> Setup</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> .. _Bioconda: https://bioconda.github.io</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> .. _Vagrant: https://www.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> .. _Vagrant Documentation: https://docs.vagrantup.com</span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Blogpost: http://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Blogpost: https://blog.osteel.me/posts/2015/01/25/how-to-use-vagrant-on-windows.html</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> Requirements</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> ::::::::::::</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/short.rst b/docs/tutorial/short.rst</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gh" style="color: #999;">index ab4d3a7f..95571f73 100644</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/short.rst</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/short.rst</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="p">@@ -184,12 +184,12 @@</span> variants. First, we define a variable</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> at the top of the ``Snakefile``. This serves as a definition of the</span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> samples over which we would want to aggregate. In real life, you would</span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> want to use an external sample sheet or a `config</span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-file <http://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#step-2-config-files>`__</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+file <https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#step-2-config-files>`__</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"> for things like this.</span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> For aggregation over many files, Snakemake provides the helper function</span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> ``expand`` (see `the</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-docs <http://snakemake.readthedocs.io/en/stable/tutorial/basics.html#step-5-calling-genomic-variants>`__).</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+docs <https://snakemake.readthedocs.io/en/stable/tutorial/basics.html#step-5-calling-genomic-variants>`__).</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> Create a rule ``call`` with input files</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> - ``fa="data/genome.fa"``</span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/docs/tutorial/tutorial.rst b/docs/tutorial/tutorial.rst</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gh" style="color: #999;">index 768ead56..00b655f5 100644</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/tutorial/tutorial.rst</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/tutorial/tutorial.rst</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="p">@@ -4,10 +4,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> Snakemake Tutorial</span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> ==================</span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Snakemake: http://snakemake.readthedocs.io</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Snakemake: https://snakemake.readthedocs.io</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> .. _GNU Make: https://www.gnu.org/software/make</span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _Python: http://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.. _slides: http://slides.com/johanneskoester/snakemake-tutorial</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _Python: https://www.python.org</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.. _slides: https://slides.com/johanneskoester/snakemake-tutorial</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> .. _Conda: https://conda.io</span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> .. _Singularity: https://www.sylabs.io</span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/gui.html b/snakemake/gui.html</span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/gui.html</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> body {</span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/io.py b/snakemake/io.py</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gh" style="color: #999;">index ff149c3c..2b3a30f9 100755</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/io.py</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/io.py</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="p">@@ -1355,7 +1355,7 @@</span> def _load_configfile(configpath, filetype="Config"):</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> except ValueError:</span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> f.seek(0) # try again</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # From http://stackoverflow.com/a/21912744/84349</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # From https://stackoverflow.com/a/21912744/84349</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> class OrderedLoader(yaml.Loader):</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> pass</span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/remote/NCBI.py b/snakemake/remote/NCBI.py</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gh" style="color: #999;">index b232dd77..a64428bc 100644</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/remote/NCBI.py</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/remote/NCBI.py</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="p">@@ -443,7 +443,7 @@</span> class NCBIHelper(object):</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> def parse_accession_str(self, id_str):</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> """</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> This tries to match an NCBI accession as defined here:</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http://www.ncbi.nlm.nih.gov/Sequin/acc.html</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ https://www.ncbi.nlm.nih.gov/Sequin/acc.html</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> m = re.search(</span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> r"(?P<accession>(?:[a-zA-Z]{1,6}|NW_|NC_|NM_|NR_)\d{1,10})(?:\.(?P<version>\d+))?(?:\.(?P<file_ext>\S+))?.*",</span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="p">@@ -467,7 +467,7 @@</span> class NCBIHelper(object):</span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> @staticmethod</span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> def _seq_chunks(seq, n):</span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # http://stackoverflow.com/a/312464/190597 (Ned Batchelder)</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # https://stackoverflow.com/a/312464/190597 (Ned Batchelder)</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> """ Yield successive n-sized chunks from seq."""</span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> for i in range(0, len(seq), n):</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> yield seq[i : i + n]</span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/snakemake/utils.py b/snakemake/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gh" style="color: #999;">index 451c25ca..7edadc2e 100644</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="p">@@ -31,10 +31,10 @@</span> def validate(data, schema, set_default=True):</span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> schema (str): Path to JSON schema used for validation. The schema can also be</span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"> in YAML format. If validating a pandas data frame, the schema has to</span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> describe a row record (i.e., a dict with column names as keys pointing</span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- to row values). See http://json-schema.org. The path is interpreted</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ to row values). See https://json-schema.org. The path is interpreted</span></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> relative to the Snakefile when this function is called.</span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> set_default (bool): set default values defined in schema. See</span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http://python-jsonschema.readthedocs.io/en/latest/faq/ for more</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ https://python-jsonschema.readthedocs.io/en/latest/faq/ for more</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> information</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> """</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="p">@@ -61,7 +61,7 @@</span> def validate(data, schema, set_default=True):</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"> handlers={"file": lambda uri: _load_configfile(re.sub("^file://", "", uri))},</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Taken from http://python-jsonschema.readthedocs.io/en/latest/faq/</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Taken from https://python-jsonschema.readthedocs.io/en/latest/faq/</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> def extend_with_default(validator_class):</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> validate_properties = validator_class.VALIDATORS["properties"]</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="p">@@ -450,7 +450,7 @@</span> def update_config(config, overwrite_config):</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> """Recursively update dictionary config with overwrite_config.</span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> See</span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- http://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> for details.</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> </span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> Args:</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="p">@@ -477,7 +477,7 @@</span> def available_cpu_count():</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> when the cpuset(7) mechanism is in use, as is the case on some cluster</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> systems.</span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Adapted from http://stackoverflow.com/a/1006301/715090</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Adapted from https://stackoverflow.com/a/1006301/715090</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> with open("/proc/self/status") as f:</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/versioneer.py b/versioneer.py</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gh" style="color: #999;">index 64fea1c8..a9dba122 100644</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/versioneer.py</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/versioneer.py</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="p">@@ -1752,7 +1752,7 @@</span> def do_setup():</span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> except EnvironmentError:</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> pass</span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> # That doesn't cover everything MANIFEST.in can do</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # (http://docs.python.org/2/distutils/sourcedist.html#commands), so</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # (https://docs.python.org/2/distutils/sourcedist.html#commands), so</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> # it might give some false negatives. Appending redundant 'include'</span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> # lines is safe, though.</span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"> if "versioneer.py" not in simple_includes:</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,3 +6,5 @@ local_javascript.patch</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">0009-skip-test-without-google-cloud-sdk.patch</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">python3.patch</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">workaround_sphinx_issue.patch</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">link_security.patch</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">bug322_cluster_sync.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#260fb267aa59c740952b443e87e306a192a8d82e"><strong>debian/patches/workaround_sphinx_issue.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: "Rebecca N. Palmer" <rebecca_palmer@zoho.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Date: Wed, 8 Apr 2020 22:13:19 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Exclude common.py:lazy_property from documentation</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Needed as Sphinx 2 can't process it</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">This is obviously not an ideal fix, but it's an internal class with little</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">documentation to begin with:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/955056</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: An upstream comment says common.py:lazy_property is the problem item, </span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> and excluding that from the documentation does make Sphinx succeed (I </span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> haven't tested a whole build):</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> This is obviously not an ideal fix, but it's an internal class with little</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> documentation to begin with: https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">Forwarded: https://github.com/snakemake/snakemake/issues/296#issuecomment-611197453</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff">--- a/docs/conf.py</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/conf.py</span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container<span class="idiff left right"> and not test_cluster_sync</span>'</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># test_report</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># test_ancient</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,6 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k</td>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># test_env_modules relies on "module load" which is not packaged for Debian</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># test_archive uses conda</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># test_container uses docker://bash</span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"># test_cluster_sync is broken (https://github.com/snakemake/snakemake/issues/322)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/</span>
</pre>
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27
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/e7d154fa5c24b5873740cbdafc72920f1660f3c9...7d50f8d318478b6bb767b008c540da954f4fc92a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-n</span> auto <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container<span class="idiff left right"> and not test_cluster_sync</span>'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-n</span> auto <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span></pre>
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