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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/covpipe">Debian Med / covpipe</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/f50c03dcc729b49f2ad4700cf2a335330f233250">f50c03dc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.6</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/f3bcba61b00a7426d4e82a3a6bbaa8752f320e7f">f3bcba61</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/4f1f40a73d46da5842c7f18a6d0145f9eb5ae4c5">4f1f40a7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.0.6'
Update to upstream version '3.0.6'
with Debian dir 95f7f1e96193337a116877d061c907830953c9f8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/f7bfa16ffe95e96af16d96b6ae28b55f4515bb36">f7bfa16f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/fd858b3362923799899f405568aa628dea849447">fd858b33</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:38:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covpipe/-/commit/0ac2b6e6bc7129f2451763e584b80b9ea723dd0d">0ac2b6e6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-15T09:40:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unused test, cleanup changelog
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#c0d67716a4ccb1ddb1295b3168e55a5279d1baa4">
<span class="new-file">
+
.conda/3.0.3/build.sh
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<li class="file-stats">
<a href="#9306975c462aacafd98eb240ab148e59789541f3">
<span class="new-file">
+
.conda/3.0.3/meta.yaml
</span>
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<li class="file-stats">
<a href="#5044e218499824a1c39357ce1c4912e15dfed81c">
<span class="new-file">
+
.conda/3.0.4/build.sh
</span>
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<li class="file-stats">
<a href="#1d2195ae93fa43118fe1e31a7cd247a84c48e11f">
<span class="new-file">
+
.conda/3.0.4/meta.yaml
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<li class="file-stats">
<a href="#e8981d8aba3d5776b234404fe87a235b30f1b4f3">
<span class="new-file">
+
.conda/3.0.5/build.sh
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<li class="file-stats">
<a href="#a2c1f4fd11af11ac9c8c713cbbb49881538362ac">
<span class="new-file">
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.conda/3.0.5/meta.yaml
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<li class="file-stats">
<a href="#d257ba2aa1e53f638eeeafd0740bb03d350917fc">
.conda/meta.yaml
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<li class="file-stats">
<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">
.gitlab-ci.yml
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<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#597ee46638e91ade71d0651e36532ab84c30fcb1">
covpipe/__version__.py
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<li class="file-stats">
<a href="#72689fc391b930e2f46a05a96f44728e8f62876d">
covpipe/ncov_minipipe.Rmd
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<li class="file-stats">
<a href="#d051687e18203812decae43018b3bd6ecf28804f">
covpipe/ncov_minipipe.config
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<li class="file-stats">
<a href="#622a6ad92f0f17016033d2e2a3034b6709a24faf">
covpipe/ncov_minipipe.py
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<li class="file-stats">
<a href="#838ab6c5a4748a40ff545721edd87ac5d144dd0f">
covpipe/ncov_minipipe.snake
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<li class="file-stats">
<a href="#80f2e49a40c26133b9b6bcdfcf08efdfa2247a37">
covpipe/rules/assign_lineage.smk
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<li class="file-stats">
<a href="#491269433cdc279dd18f2793a30f11bf9abf9a55">
covpipe/rules/classify_reads.smk
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<li class="file-stats">
<a href="#d775516cdb3f3ec1ad8cb5e542e7cab3c007df47">
covpipe/rules/get_version.smk
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<li class="file-stats">
<a href="#dca120fe48a8f069b9b95e3209aa9f51daccc7d9">
covpipe/rules/trim_reads.smk
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<li class="file-stats">
<a href="#4b2465b2029aef2dcee63d208c5b8609d5678dbd">
covpipe_env.yaml
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<li class="file-stats">
<a href="#3f60363c5cb77eeb90e9a3f00e6ab04919814822">
<span class="new-file">
+
covpipe_tools/primerbed2bedpe.py
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</a>
</li>
<li class="file-stats">
<a href="#ee30b68dd2215790f03019a13c78092a44587207">
covpipe_tools/update_pangolin.py
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#6bf1ea907d47c5d7ef0130ef1f1ff3f1ef267ac7">
<span class="deleted-file">
−
debian/tests/control_deactivated
</span>
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="deleted-file">
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debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
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debian/upstream/metadata
</span>
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</li>
<li class="file-stats">
<a href="#97d42055d8a8ae104887701fdda7934b652e6192">
ncov_minipipe.conda.setup/setup_env.sh
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</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#7cc23430d3e061a3235f9c707657bbeea004459f">
tests/TestData/GEN_SAMPLES/mixture.csv
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</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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