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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/f8a1a562c9b43ccd7376ec48ac5f155cecaf313f">f8a1a562</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-12-11T10:15:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/1396015f11e3821e4dc9828cf78a13142b09c6b0">1396015f</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-12-11T10:16:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.9'
Update to upstream version '1.1.9'
with Debian dir 1c04d3ef7455100580dc4c5f1870b80f25082d30</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/39e6763084c5cccc0439e05924ea68ea9eccdeef">39e67630</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-12-11T14:06:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version - sadly few changes on our side
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
</a>
</li>
<li class="file-stats">
<a href="#059a93c69080af2f6054c5324203b7af73cc5b83">
bcbio/bam/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#db6099147d782b81be3efa804f6a41b2a6b7ebf5">
bcbio/broad/picardrun.py
</a>
</li>
<li class="file-stats">
<a href="#fb17eef4888c4f7198909ebc1616eb92a3fed380">
bcbio/chipseq/__init__.py
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</li>
<li class="file-stats">
<a href="#e058999dc6b36492007fce47afb7a70ca8b25e3d">
<span class="new-file">
+
bcbio/chipseq/atac.py
</span>
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<li class="file-stats">
<a href="#4eabad8cbe351e3e3d7466ee25d9d970b164368a">
bcbio/chipseq/macs2.py
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<li class="file-stats">
<a href="#fbfb96675c481efdacfedf0214b473e7d623d79c">
bcbio/chipseq/peaks.py
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</li>
<li class="file-stats">
<a href="#fee19f4f498a2b34eca43fa79376fa526f252577">
bcbio/heterogeneity/chromhacks.py
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</li>
<li class="file-stats">
<a href="#037a5da84cee54d04c6672861c844615a844912f">
bcbio/ngsalign/bwa.py
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<li class="file-stats">
<a href="#bbb7842f2be9690f4ae67a1de2c07f322d6e261e">
bcbio/ngsalign/star.py
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</li>
<li class="file-stats">
<a href="#28669a7ddccdf8ac47c577727840379bba16c871">
bcbio/pipeline/rnaseq.py
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</li>
<li class="file-stats">
<a href="#6a5842dd9e3c5daac8e6d62a34e4d60ab86b78bf">
bcbio/pipeline/run_info.py
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<li class="file-stats">
<a href="#fac91f905233560f253b7063f3b6889aeca3af62">
bcbio/pipeline/sample.py
</a>
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<li class="file-stats">
<a href="#0b928052acb70b506a8457627983f038aaf8fd4d">
bcbio/qc/multiqc.py
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</li>
<li class="file-stats">
<a href="#1632995720dec2c83890f793045a09678042e862">
bcbio/qc/viral.py
</a>
</li>
<li class="file-stats">
<a href="#953a5484c194dec73486a5e85ad272cd898cbf31">
bcbio/upload/__init__.py
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<li class="file-stats">
<a href="#b5f97c2465c41ae9654e19860697f479dc1cf205">
bcbio/variation/effects.py
</a>
</li>
<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#f1753c26ad7dd9c07a75161a266af4cb354610d3">
docs/contents/configuration.rst
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</li>
<li class="file-stats">
<a href="#46caee1d50ca05a5fb7d450ccc1f3934ae0c9bc3">
docs/contents/internals.rst
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</li>
<li class="file-stats">
<a href="#25f1fbed65859fbfcdb276507ddb9f56ebb11056">
docs/contents/outputs.rst
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<li class="file-stats">
<a href="#b1655f936472b3a6a6a310218f78e1d19987454b">
requirements-conda.txt
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</li>
<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
</a>
</li>
<li class="file-stats">
<a href="#bacc76312ae1e30f71298a0e5abf86c8e5dbec70">
scripts/bcbio_setup_genome.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
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<li class="file-stats">
<a href="#c493fa11b32390866834a9938a57d281ac430b70">
<span class="new-file">
+
tests/data/atac/atac_1.fq
</span>
</a>
</li>
<li class="file-stats">
<a href="#4996eb58871bb817700228bd24171ab56ceaa95c">
<span class="new-file">
+
tests/data/atac/atac_2.fq
</span>
</a>
</li>
<li class="file-stats">
<a href="#ca1b3dbd209bf79f801b5a187faa2998b349c033">
<span class="new-file">
+
tests/data/automated/run_info-atacseq.yaml
</span>
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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