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<h3>
Andreas Tille pushed to branch upstream
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/d5ce6effe383044853259316c374a35244766f06">d5ce6eff</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-03T10:38:21+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.15.1</pre>
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<h4>29 changed files:</h4>
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<li class="file-stats">
<a href="#cd3fd8615ae98556916b352d1dff137ff81c4027">
docs/executor_tutorial/tutorial.rst
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<a href="#9b54be2cff8d0de677b1245d0b0dc07cca021923">
docs/snakefiles/configuration.rst
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<li class="file-stats">
<a href="#945ec74fc1c17902d98bca84b7a1f0dfd755c01b">
docs/snakefiles/deployment.rst
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<a href="#dfeb7b6e739ba66056c1799c63a5a39c7698b59f">
docs/snakefiles/rules.rst
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<li class="file-stats">
<a href="#d366205d7cd679ff6d4a61f70728e92537101763">
snakemake/__init__.py
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<a href="#5e16cbeea010f59dbef52f8950f4873c94f39c7e">
snakemake/_version.py
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<li class="file-stats">
<a href="#1f2b5ab7db93d7cfd11a4660dfd26daffc5b38dc">
snakemake/caching/__init__.py
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<a href="#5752dcb5dceb2252f447b747551b9e646cf1865e">
snakemake/caching/local.py
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<a href="#9821437dfb3fff8383b6066a2a3c7aa3f6712a32">
snakemake/dag.py
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<a href="#f15af42c37739d075863d61c80d393b9af0c346c">
snakemake/deployment/conda.py
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<a href="#8a638600ab5121801770ac0563c30576f0b2032b">
snakemake/modules.py
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snakemake/notebook.py
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<a href="#d70c11793454d64a7b2d77ced116226d2f13378e">
snakemake/parser.py
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snakemake/report/__init__.py
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<a href="#eacfcbe8d8cfc248830fb72e5b857992bc8b3b76">
snakemake/ruleinfo.py
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<a href="#cb9e107597e441fb1c0d61663359d9cf1dbfe04d">
snakemake/workflow.py
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tests/test_cache_multioutput/Snakefile
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tests/test_cache_multioutput/expected-results/.gitkeep
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tests/test_default_target/Snakefile
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tests/test_default_target/expected-results/1.txt
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tests/test_default_target/expected-results/2.txt
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tests/test_deploy_hashing/Snakefile
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tests/test_deploy_hashing/a.post-deploy.sh
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tests/test_deploy_hashing/a.yaml
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tests/test_deploy_hashing/b.yaml
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tests/test_deploy_hashing/expected-results/a.txt
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tests/test_deploy_hashing/expected-results/b.txt
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<a href="#002e3bc3eddf51d9e25c30326a4bc060aadbf93b">
tests/tests.py
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Changelog</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### [6.15.1](https://www.github.com/snakemake/snakemake/compare/v6.15.0...v6.15.1) (2022-01-31)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
</pre>
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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="LC5" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="3" 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="new_line diff-line-num new" data-linenumber="6" 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="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="3" 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="new_line diff-line-num new" data-linenumber="8" 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="LC8" class="line" lang="markdown"><span class="p">*</span> consider post-deploy script for env hashing (<span class="p">[</span><span class="nv" style="color: #008080;">#1363</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1363</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">d50efd9</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/d50efd9d16d029fb0e5b14b182882c71a20552bb</span><span class="p">)</span>)</span>
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<td class="new_line diff-line-num new" data-linenumber="9" 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="LC9" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" 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">
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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="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [6.15.0](https://www.github.com/snakemake/snakemake/compare/v6.14.0...v6.15.0) (2022-01-29)</span></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="12" 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="LC12" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Features</span></span>
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<td class="new_line diff-line-num new" 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="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" 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="LC15" class="line" lang="markdown"><span class="p">*</span> adding default_target directive for declaring default target rules that are not the first rule in the workflow. (<span class="p">[</span><span class="nv" style="color: #008080;">#1358</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1358</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">638ec1a</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/638ec1a983741cd7ba8faaf1a9dc76ae43d012e5</span><span class="p">)</span>)</span>
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<td class="new_line diff-line-num new" data-linenumber="16" 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="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug Fixes</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> Draft notebook filename with wildcards and params. (<span class="p">[</span><span class="nv" style="color: #008080;">#1352</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1352</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">11d4dc8</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/11d4dc88598ffb901450bd4e076b91f4e27d37b0</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">*</span> proper error message when defining cache eligibility for rules with multiple output files and no multiext declaration. (<span class="p">[</span><span class="nv" style="color: #008080;">#1357</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1357</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">47b5096</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/47b5096ebbdd3d94a9c99b443064b1b0de389c64</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Documentation</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">*</span> Command line arguments for configuration files (<span class="p">[</span><span class="nv" style="color: #008080;">#1343</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1343</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">ad8aaa4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/ad8aaa4853a150211513baecc474956575d326eb</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">*</span> fix broken link in executor_tutorial/tutorial.rst (<span class="p">[</span><span class="nv" style="color: #008080;">#1360</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/issues/1360</span><span class="p">)</span>) (<span class="p">[</span><span class="nv" style="color: #008080;">c9be764</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/snakemake/snakemake/commit/c9be76482d05577c4b1528b0e52ba15fc17a1dd5</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [6.14.0](https://www.github.com/snakemake/snakemake/compare/v6.13.1...v6.14.0) (2022-01-26)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#cd3fd8615ae98556916b352d1dff137ff81c4027"><strong>docs/executor_tutorial/tutorial.rst</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Snakemake Executor Tutorials</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">============================</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.. _cloud executors: https://snakemake.readthedocs.io/en/stable/executing/<span class="idiff left right">cluster-</span>cloud.html</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.. _cloud executors: https://snakemake.readthedocs.io/en/stable/executing/cloud.html</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.. _tutorial: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">This set of tutorials are intended to introduce you to executing `cloud executors`_.</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#9b54be2cff8d0de677b1245d0b0dc07cca021923"><strong>docs/snakefiles/configuration.rst</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">@@ -37,10 +37,10 @@ In addition to the `configfile` statement, config values can be overwritten via</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> $ snakemake --config yourparam=1.5</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Further, you can manually alter the config dictionary using any Python code **outside** of your rules. Changes made from within a rule won't be seen from other rules.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Finally, you can use the `--configfile` command line argument to overwrite values from the `configfile` statement.</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Note that any values parsed into the `config` dictionary with any of above mechanisms are merged, i.e., all keys defined via a `configfile`</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">statement, or the `--configfile` and `--config` command line arguments will end up in the final `config` dictionary, but if two methods define the same key, command line</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">overwrites the `configfile` statement.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Finally, you can use the <span class="idiff left">`</span>`--configfile`<span class="idiff right">`</span> command line argument to overwrite values from the `configfile` statement.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Note that any values parsed into the <span class="idiff left">`</span>`config`<span class="idiff">`</span> dictionary with any of above mechanisms are merged, i.e., all keys defined via a <span class="idiff">`</span>`configfile`<span class="idiff right">`</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">statement, or the <span class="idiff left">`</span>`--configfile`<span class="idiff">`</span> and <span class="idiff">`</span>`--config`<span class="idiff right">`</span> command line arguments will end up in the final `config` dictionary, but if two methods define the same key, command line</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">overwrites the <span class="idiff left">`</span>`configfile`<span class="idiff right">`</span> statement.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">For adding config placeholders into a shell command, Python string formatting syntax requires you to leave out the quotes around the key name, like so:</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#945ec74fc1c17902d98bca84b7a1f0dfd755c01b"><strong>docs/snakefiles/deployment.rst</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">@@ -103,7 +103,7 @@ For example, we can easily add another rule to extend the given workflow:</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> github("snakemake-workflows/dna-seq-gatk-variant-calling", path="workflow/Snakefile", tag="v2.0.1")</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> config: config</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> use rule * from dna_seq</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> use rule * from dna_seq<span class="idiff left right"> as dna_seq_*</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> # easily extend the workflow</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> rule plot_vafs:</span>
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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">@@ -114,7 +114,19 @@ For example, we can easily add another rule to extend the given workflow:</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> notebook:</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext"> "notebooks/plot-vafs.py.ipynb"</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">Moreover, it is possible to further extend the workflow with other modules, thereby generating an integrative analysis.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> # Define a new default target that collects both the targets from the dna_seq module as well as</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> # the new plot.</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> rule all:</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> rules.dna_seq_all.input,</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> "results/plots/vafs.svg",</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> default_target: True</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">Above, we have added a prefix to all rule names of the dna_seq module, such that there is no name clash with the added rules (``as dna_seq_*`` in the ``use rule`` statement).</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">In addition, we have added a new rule ``all``, defining the default target in case the workflow is executed (as usually) without any specific target files or rule.</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">The new target rule collects both all input files of the rule ``all`` from the dna_seq workflow, as well as additionally collecting the new plot.</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">It is possible to further extend the workflow with other modules, thereby generating an integrative analysis.</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">Here, let us assume that we want to conduct another kind of analysis, say RNA-seq, using a different external workflow.</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext">We can extend above example in the following way:</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"></span>
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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">@@ -149,10 +161,20 @@ We can extend above example in the following way:</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> use rule * from rna_seq as rna_seq_*</span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext">Above, several things have changed. First, we have added another module ``rna_seq``.</span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext">Second, we have added a prefix to all rule names of both modules (``dna_seq_*`` and ``rna_seq_*`` in the ``use rule`` statements) in order to avoid rule name clashes.</span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">Third, we have added a prefix to all non-absolute input and output file names of both modules (``prefix: "dna-seq"`` and ``prefix: "rna-seq"``) in order to avoid file name clashes.</span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">Finally, we provide the config of the two modules via two separate sections in the common config file (``config["dna-seq"]`` and ``config["rna-seq"]``).</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> # Define a new default target that collects all the targets from the dna_seq and rna_seq module.</span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> rule all:</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> rules.dna_seq_all.input,</span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> rules.rna_seq_all.input,</span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> default_target: True</span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">Above, several things have changed. </span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">* First, we have added another module ``rna_seq``.</span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">* Second, we have added a prefix to all non-absolute input and output file names of both modules (``prefix: "dna-seq"`` and ``prefix: "rna-seq"``) in order to avoid file name clashes.</span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">* Third, we have added a default target rule that collects both the default targets from the module ``dna_seq`` as well as the module ``rna_seq``.</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">* Finally, we provide the config of the two modules via two separate sections in the common config file (``config["dna-seq"]`` and ``config["rna-seq"]``).</span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">----------------------------------</span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">Uploading workflows to WorkflowHub</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#dfeb7b6e739ba66056c1799c63a5a39c7698b59f"><strong>docs/snakefiles/rules.rst</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">@@ -246,11 +246,25 @@ By default snakemake executes the first rule in the snakefile. This gives rise t</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext"> rule all:</span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="plaintext"> input: ["{dataset}/file.A.txt".format(dataset=dataset) for dataset in DATASETS]</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> expand("{dataset}/file.A.txt", dataset=DATASETS)</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">Here, for each dataset in a python list ``DATASETS`` defined before, the file ``{dataset}/file.A.txt`` is requested.</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">In this example, Snakemake recognizes automatically that these can be created by multiple applications of the rule ``complex_conversion`` shown above.</span>
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250
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">It is possible to overwrite this behavior to use the first rule as a default target, by explicitly marking a rule as being the default target via the ``default_target`` directive:</span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="plaintext">Here, for each dataset in a python list ``DATASETS`` defined before, the file ``{dataset}/file.A.txt`` is requested. In this example, Snakemake recognizes automatically that these can be created by multiple applications of the rule ``complex_conversion`` shown above.</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> rule xy:</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> expand("{dataset}/file.A.txt", dataset=DATASETS)</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> default_target: True</span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">Regardless of where this rule appears in the Snakefile, it will be the default target.</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">Usually, it is still recommended to keep the default target rule (and in fact all other rules that could act as optional targets) at the top of the file, such that it can be easily found.</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">The ``default_target`` directive becomes particularly useful when :ref:`combining several pre-existing workflows <use_with_modules>`.</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext">.. _snakefiles-threads:</span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#d366205d7cd679ff6d4a61f70728e92537101763"><strong>snakemake/__init__.py</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">@@ -591,7 +591,9 @@ def snakemake(</td>
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">include</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">snakefile</span><span class="p">,</span> <span class="n" style="color: #333;">overwrite_first_rule</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">print_compilation</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_compilation</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">snakefile</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">overwrite_default_target</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="n" style="color: #333;">print_compilation</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_compilation</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">check</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#5e16cbeea010f59dbef52f8950f4873c94f39c7e"><strong>snakemake/_version.py</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">@@ -22,9 +22,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> main, tag: v6.1<span class="idiff left right">4.0</span>)"</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left">6</span>c5<span class="idiff right">05c290facddbc44da69d715e90b7680ad9ceb</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2022-01-<span class="idiff left right">26 11:32:12</span> +0100"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (HEAD -> main, tag: v6.1<span class="idiff left right">5.1</span>)"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left">8</span>c5<span class="idiff right">c5e8261ae12fc40c3c293045dea6af7df0e01</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2022-01-<span class="idiff left right">31 12:10:44</span> +0100"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#1f2b5ab7db93d7cfd11a4660dfd26daffc5b38dc"><strong>snakemake/caching/__init__.py</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">@@ -47,6 +47,9 @@ class AbstractOutputFileCache:</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="p">((</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">prefix_len</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="p">),</span> <span class="s" style="color: #d14;">"bug: multiple output files in cacheable job but multiext not used for declaring them"</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">raise_write_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span><span class="p">,</span> <span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#5752dcb5dceb2252f447b747551b9e646cf1865e"><strong>snakemake/caching/local.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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>
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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">@@ -95,6 +95,12 @@ class OutputFileCache(AbstractOutputFileCache):</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">cachefile</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">raise_cache_miss_exception</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"Output file {} exists as {} in the cache."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="n" style="color: #333;">cachefile</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_readable</span><span class="p">(</span><span class="n" style="color: #333;">cachefile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cachefile</span><span class="p">.</span><span class="n" style="color: #333;">is_dir</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For directories, create a new one and symlink each entry.</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#9821437dfb3fff8383b6066a2a3c7aa3f6712a32"><strong>snakemake/dag.py</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">@@ -622,7 +622,7 @@ class DAG:</td>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">is_checkpoint</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">targetjobs</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">first_rule</span></span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">default_target</span></span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">tempfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#f15af42c37739d075863d61c80d393b9af0c346c"><strong>snakemake/deployment/conda.py</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">@@ -62,8 +62,14 @@ class Env:</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">env_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infer_source_file</span><span class="p">(</span><span class="n" style="color: #333;">env_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">get_path_or_uri</span><span class="p">()).</span><span class="n" style="color: #333;">with_suffix</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">".post-deploy.sh"</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">deploy_file</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infer_source_file</span><span class="p">(</span><span class="n" style="color: #333;">deploy_file</span><span class="p">)</span></span>
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67
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">env_name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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68
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">env_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"bug: both env_file and env_name specified"</span></span>
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69
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">env_name</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" 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="107" 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">@@ -101,8 +107,9 @@ class Env:</td>
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101
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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102
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_content_deploy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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103
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_is_file_based</span><span class="p">()</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">).</span><span class="n" style="color: #333;">with_suffix</span><span class="p">(</span><span class="s" style="color: #d14;">".post-deploy.sh"</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">sourcecache</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">deploy_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">sourcecache</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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106
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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107
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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108
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_env_archive_dir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" 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="146" 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">@@ -139,6 +146,9 @@ class Env:</td>
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139
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">env_dir</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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140
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_container_img</span><span class="p">:</span></span>
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141
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_container_img</span><span class="p">.</span><span class="n" style="color: #333;">url</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">content_deploy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">content_deploy</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">content_deploy</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">content_deploy</span><span class="p">)</span></span>
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142
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">content</span><span class="p">)</span></span>
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143
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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144
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hash</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="158" 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">@@ -148,6 +158,9 @@ class Env:</td>
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148
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_content_hash</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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149
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">()</span></span>
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150
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">content</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">content_deploy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">content_deploy</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">content_deploy</span><span class="p">:</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">content_deploy</span><span class="p">)</span></span>
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151
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_content_hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">md5hash</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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152
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_content_hash</span></span>
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153
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="317" 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="330" 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">@@ -317,11 +330,7 @@ class Env:</td>
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317
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">content</span><span class="p">)</span></span>
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318
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">env_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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319
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">tmp_env_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">get_path_or_uri</span><span class="p">())</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">with_suffix</span><span class="p">(</span><span class="s" style="color: #d14;">".post-deploy.sh"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">delete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">".post-deploy.sh"</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tmp</span><span class="p">:</span></span>
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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">@@ -331,8 +340,7 @@ class Env:</td>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">tmp_deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">env_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">env_file</span><span class="p">.</span><span class="n" style="color: #333;">get_path_or_uri</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">env_file</span><span class="p">).</span><span class="n" style="color: #333;">with_suffix</span><span class="p">(</span><span class="s" style="color: #d14;">".post-deploy.sh"</span><span class="p">).</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">env_file</span><span class="p">).</span><span class="n" style="color: #333;">with_suffix</span><span class="p">(</span><span class="s" style="color: #d14;">".post-deploy.sh"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">deploy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">post_deploy_file</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">env_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">address</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#8a638600ab5121801770ac0563c30576f0b2032b"><strong>snakemake/modules.py</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">@@ -86,7 +86,7 @@ class ModuleInfo:</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">replace_wrapper_tag</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_wrapper_tag</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">include</span><span class="p">(</span><span class="n" style="color: #333;">snakefile</span><span class="p">,</span> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">first_rule</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">include</span><span class="p">(</span><span class="n" style="color: #333;">snakefile</span><span class="p">,</span> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">default_target</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_snakefile</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">meta_wrapper</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#87b26159067ade1d989921cb3240bfabece3aea0"><strong>snakemake/notebook.py</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">@@ -13,6 +13,7 @@ from snakemake.logging import logger</td>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">is_local_file</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.common</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ON_WINDOWS</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.sourcecache</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SourceCache</span><span class="p">,</span> <span class="n" style="color: #333;">infer_source_file</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">format</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">KERNEL_STARTED_RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"Kernel started: (?P<kernel_id>\S+)"</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">KERNEL_SHUTDOWN_RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"Kernel shutdown: (?P<kernel_id>\S+)"</span><span class="p">)</span></span>
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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">@@ -262,6 +263,7 @@ def notebook(</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;"> Load a script from the given basedir + path and execute it.</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">draft</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">wildcards</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wildcards</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_local_file</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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267
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isabs</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<li id="d70c11793454d64a7b2d77ced116226d2f13378e">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#d70c11793454d64a7b2d77ced116226d2f13378e"><strong>snakemake/parser.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="484" 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">@@ -484,6 +484,12 @@ class Cache(RuleKeywordState):</td>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"cache_rule"</span></span>
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DefaultTarget</span><span class="p">(</span><span class="n" style="color: #333;">RuleKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">keyword</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"default_target_rule"</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Handover</span><span class="p">(</span><span class="n" style="color: #333;">RuleKeywordState</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"></span>
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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">@@ -673,6 +679,7 @@ rule_property_subautomata = dict(</td>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Group</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">cache</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Cache</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">handover</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Handover</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">default_target</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">DefaultTarget</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"></span>
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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">@@ -281,7 +281,11 @@ class RuleRecord:</td>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">notebook</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">script</span><span class="p">.</span><span class="n" style="color: #333;">get_source</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">notebook</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">sourcecache</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">basedir</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">notebook</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">sourcecache</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rule</span><span class="p">.</span><span class="n" style="color: #333;">basedir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">wildcards</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">wildcards</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">params</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">language</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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287
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">notebook</span><span class="p">.</span><span class="n" style="color: #333;">get_cell_sources</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#eacfcbe8d8cfc248830fb72e5b857992bc8b3b76"><strong>snakemake/ruleinfo.py</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">@@ -37,6 +37,7 @@ class RuleInfo:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cache</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path_modifier</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">handover</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">apply_modifier</span><span class="p">(</span></span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">,</span> <span class="n" style="color: #333;">prefix_replacables</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"input"</span><span class="p">,</span> <span class="s" style="color: #d14;">"output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"log"</span><span class="p">,</span> <span class="s" style="color: #d14;">"benchmark"</span><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#cb9e107597e441fb1c0d61663359d9cf1dbfe04d"><strong>snakemake/workflow.py</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">@@ -155,7 +155,7 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">[</span><span class="s" style="color: #d14;">"_nodes"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nodes</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">first_rule</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">default_target</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_workdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overwrite_workdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overwrite_workdir</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workdir_init</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">curdir</span><span class="p">)</span></span>
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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">@@ -466,8 +466,8 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rules</span><span class="p">[</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">is_overwrite</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rule_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">first_rule</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">first_rule</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">default_target</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">default_target</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_rule</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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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">@@ -644,7 +644,9 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">relpath</span><span class="p">,</span> <span class="n" style="color: #333;">filterfalse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_rule</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">targets</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">first_rule</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">first_rule</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="p">)</span></span>
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prioritytargets</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">prioritytargets</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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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">@@ -1148,7 +1150,7 @@ class Workflow:</td>
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">include</span><span class="p">(</span></span>
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1149
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1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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1150
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1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="python"> <span class="n" style="color: #333;">snakefile</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1151" class="line" lang="python"> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">first_rule</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="python"> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">default_target</span></span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="python"> <span class="n" style="color: #333;">print_compilation</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="python"> <span class="n" style="color: #333;">overwrite_shellcmd</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="python"> <span class="p">):</span></span>
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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">@@ -1164,7 +1166,7 @@ class Workflow:</td>
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1164
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">snakefile</span><span class="p">)</span></span>
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1165
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_stack</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">snakefile</span><span class="p">)</span></span>
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1168
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<pre style="margin: 0;"> <span id="LC1168" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">first_rule</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">first_rule</span></span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">default_target</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">default_target</span></span></span>
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="python"> <span class="n" style="color: #333;">code</span><span class="p">,</span> <span class="n" style="color: #333;">linemap</span><span class="p">,</span> <span class="n" style="color: #333;">rulecount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span></span>
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1169
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="python"> <span class="n" style="color: #333;">snakefile</span><span class="p">,</span></span>
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1170
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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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">@@ -1185,8 +1187,8 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="python"></span>
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">exec</span><span class="p">(</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">,</span> <span class="n" style="color: #333;">snakefile</span><span class="p">.</span><span class="n" style="color: #333;">get_path_or_uri</span><span class="p">(),</span> <span class="s" style="color: #d14;">"exec"</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">globals</span><span class="p">)</span></span>
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">first_rule</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">first_rule</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">first_rule</span></span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">overwrite_<span class="idiff left right">default_target</span></span><span class="p">:</span></span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">default_target</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">default_target</span></span></span>
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1190
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1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">included_stack</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>
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1191
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1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="python"></span>
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1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">onstart</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">func</span><span class="p">):</span></span>
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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">@@ -1541,6 +1543,14 @@ class Workflow:</td>
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1541
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">is_handover</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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1542
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1544
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="python"></span>
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1543
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1545
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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">cache</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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1546
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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1547
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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">is_multiext</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1548" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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1549
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<pre style="margin: 0;">+<span id="LC1549" class="line" lang="python"> <span class="s" style="color: #d14;">"Rule is marked for between workflow caching but has multiple output files. "</span></span>
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1550
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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="python"> <span class="s" style="color: #d14;">"This is only allowed if multiext() is used to declare them (see docs on between "</span></span>
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1551
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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="python"> <span class="s" style="color: #d14;">"workflow caching)."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1552" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rule</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">enable_cache</span><span class="p">:</span></span>
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1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span></span>
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1556
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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="python"> <span class="s" style="color: #d14;">"Workflow defines that rule {} is eligible for caching between workflows "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1550" 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>
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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">@@ -1550,11 +1560,20 @@ class Workflow:</td>
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1550
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1560
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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cache_rules</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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1551
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1561
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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">cache</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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1552
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1562
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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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1553
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<pre style="margin: 0;">-<span id="LC1553" class="line" lang="python"> <span class="s" style="color: #d14;">"Invalid argument for 'cache:' directive. Only <span class="idiff left right">t</span>rue allowed. "</span></span>
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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="python"> <span class="s" style="color: #d14;">"Invalid argument for 'cache:' directive. Only <span class="idiff left right">T</span>rue allowed. "</span></span>
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1554
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1564
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<pre style="margin: 0;"> <span id="LC1564" class="line" lang="python"> <span class="s" style="color: #d14;">"To deactivate caching, remove directive."</span><span class="p">,</span></span>
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1565
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rule</span><span class="p">,</span></span>
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1556
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="python"> <span class="p">)</span></span>
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1557
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="python"></span>
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1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="python"> <span class="s" style="color: #d14;">"Invalid argument for 'default_target:' directive. Only True allowed. "</span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="python"> <span class="s" style="color: #d14;">"Do not use the directive for rules that shall not be the default target. "</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="python"> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rule</span><span class="p">,</span></span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="python"> <span class="p">)</span></span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="python"></span>
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1558
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1577
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<pre style="margin: 0;"> <span id="LC1577" class="line" lang="python"> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">func</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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1559
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1578
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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">globals</span><span class="p">[</span><span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">func</span><span class="p">.</span><span class="n" style="color: #333;">__name__</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">func</span></span>
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1579
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="python"></span>
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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">@@ -1615,6 +1634,13 @@ class Workflow:</td>
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1615
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1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="python"></span>
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1616
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">decorate</span></span>
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1617
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1636
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="python"></span>
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1637
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<pre style="margin: 0;">+<span id="LC1637" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">default_target_rule</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">decorate</span><span class="p">(</span><span class="n" style="color: #333;">ruleinfo</span><span class="p">):</span></span>
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1639
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<pre style="margin: 0;">+<span id="LC1639" class="line" lang="python"> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">default_target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ruleinfo</span></span>
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1641
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="python"></span>
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1642
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<pre style="margin: 0;">+<span id="LC1642" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">decorate</span></span>
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1643
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="python"></span>
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1618
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1644
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">):</span></span>
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1619
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1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">decorate</span><span class="p">(</span><span class="n" style="color: #333;">ruleinfo</span><span class="p">):</span></span>
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1620
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="python"> <span class="n" style="color: #333;">ruleinfo</span><span class="p">.</span><span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rule a:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> output:</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> "1.txt",</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> "2.txt",</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> cache: True</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> shell:</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> "touch {output}"</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#b1eaa0f937d761ff055ec2aaeebe29137f6ce86f"><strong>tests/test_cache_multioutput/expected-results/.gitkeep</strong></a>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#f008d645ab9d7d1ddd54cde3d2593042601c703b"><strong>tests/test_default_target/Snakefile</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rule a:</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> output:</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> "{sample}.txt"</span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> shell:</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> "echo test > {output}"</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">rule b:</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> input:</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> expand("{sample}.txt", sample=[1, 2])</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> default_target: True</span></pre>
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<td class="old_line diff-line-num" 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>
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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">\ No newline at end of file</td>
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<li id="3759ad0f33decaf7015cf112f0c53f8199129423">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#3759ad0f33decaf7015cf112f0c53f8199129423"><strong>tests/test_default_target/expected-results/1.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test</span></pre>
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<li id="4cf36fcd956be980750cd730ac05b50b6d7e3c41">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#4cf36fcd956be980750cd730ac05b50b6d7e3c41"><strong>tests/test_default_target/expected-results/2.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test</span></pre>
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<li id="00bbdf67abddd40399b5c7d01b52547c49a68191">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#00bbdf67abddd40399b5c7d01b52547c49a68191"><strong>tests/test_deploy_hashing/Snakefile</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rule all:</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> input:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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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="LC3" class="line" lang="plaintext"> expand("{s}.txt", s=["a", "b"])</span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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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5
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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="LC5" class="line" lang="plaintext">rule a:</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> output:</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> "a.txt"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> conda:</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> "a.yaml"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> shell:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> "touch {output}"</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">rule b:</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> output:</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> "b.txt"</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> conda:</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> "b.yaml"</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> shell:</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> "touch {output}"</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#cf3c4d6bf615ee1ac33be5c85c62be8580116de2"><strong>tests/test_deploy_hashing/a.post-deploy.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"test"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$CONDA_PREFIX</span>/a.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#91778d520dea28137cc4a482c1607b4aedfeddd9"><strong>tests/test_deploy_hashing/a.yaml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">channels</span><span class="pi">:</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bioconda</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda-forge</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">dependencies</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python =3.10</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/d5ce6effe383044853259316c374a35244766f06#2db5ea59dd892539673460fff76eb951b911b353"><strong>tests/test_deploy_hashing/b.yaml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">channels</span><span class="pi">:</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bioconda</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda-forge</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">dependencies</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python =3.10</span></span></pre>
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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">@@ -434,6 +434,12 @@ def test_deploy_script():</td>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_deploy_script"</span><span class="p">),</span> <span class="n" style="color: #333;">use_conda</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">skip_on_windows</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_deploy_hashing</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">tmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_deploy_hashing"</span><span class="p">),</span> <span class="n" style="color: #333;">use_conda</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">cleanup</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="s" style="color: #d14;">".snakemake/conda"</span><span class="p">)))[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_conda_custom_prefix</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_conda_custom_prefix"</span><span class="p">),</span></span>
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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">@@ -1397,3 +1403,12 @@ def test_modules_ruledeps_inheritance():</td>
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">skip_on_windows</span></span>
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1404
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_conda_named</span><span class="p">():</span></span>
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_conda_named"</span><span class="p">),</span> <span class="n" style="color: #333;">use_conda</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="python"></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">skip_on_windows</span></span>
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_default_target</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_default_target"</span><span class="p">))</span></span>
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1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="python"></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="python"></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_cache_multioutput</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_cache_multioutput"</span><span class="p">),</span> <span class="n" style="color: #333;">shouldfail</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span></pre>
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