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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Lance Lin pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio" style="color: #1068bf;">Debian Med / bcbio</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bcbio/-/commit/d053e6078085c8673f1e08743ea44758f5d20ca4" style="color: #1068bf;">d053e607</a></strong>
<div>
<span>by Lance Lin</span>
<i>at 2022-08-17T20:08:13+07:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 1.2.9</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bcbio/-/commit/c3481b0ac2c2d83ba60bc57c5096411c9dae8323" style="color: #1068bf;">c3481b0a</a></strong>
<div>
<span>by Lance Lin</span>
<i>at 2022-08-17T20:08:13+07:00</i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/1.2.9'
Update to upstream version '1.2.9'
with Debian dir d922cbd6a5e4fa4585c2f0a4b7e24a94da5fa46f</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">30 changed files:</h4>
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<li class="file-stats">
<a href="#a03585ab89eed5e0782a1875b2d8153b97865d30" style="color: #1068bf;">
.github/ISSUE_TEMPLATE/bug_report.md
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<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360" style="color: #1068bf;">
HISTORY.md
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<a href="#e518229f249f53b16d0dd891314f18afa565e3cb" style="color: #1068bf;">
bcbio/broad/__init__.py
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<a href="#cf71129b76ffbf8055990dcd39c602522edf1d63" style="color: #1068bf;">
bcbio/broad/metrics.py
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<a href="#db6099147d782b81be3efa804f6a41b2a6b7ebf5" style="color: #1068bf;">
bcbio/broad/picardrun.py
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<a href="#4eabad8cbe351e3e3d7466ee25d9d970b164368a" style="color: #1068bf;">
bcbio/chipseq/macs2.py
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</li>
<li class="file-stats">
<a href="#fbfb96675c481efdacfedf0214b473e7d623d79c" style="color: #1068bf;">
bcbio/chipseq/peaks.py
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<li class="file-stats">
<a href="#1b91d366218c8601f019ee9a2c9102cdb8413c02" style="color: #1068bf;">
<span class="new-file">
+
bcbio/data/umis/harvard-indrop-v31-cb1.txt.gz
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<li class="file-stats">
<a href="#fdb443bf1bc300750f5b7e6f2087653bdd67587c" style="color: #1068bf;">
<span class="new-file">
+
bcbio/data/umis/harvard-indrop-v31-cb2.txt.gz
</span>
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<li class="file-stats">
<a href="#0e8716a471b3387b0968bddfdec6a04b4d1bcb7e" style="color: #1068bf;">
<span class="new-file">
+
bcbio/data/umis/harvard-indrop-v31-transform.json
</span>
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<li class="file-stats">
<a href="#21de3916271e785a8f3265ee5ad39597e376e1fe" style="color: #1068bf;">
bcbio/hla/optitype.py
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<li class="file-stats">
<a href="#cb1999524a51a97bd40da890cd301d883550f995" style="color: #1068bf;">
bcbio/install.py
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<a href="#df11eaca928825aa93db95fe7b7adf1aa7c3e786" style="color: #1068bf;">
bcbio/ngsalign/bismark.py
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<li class="file-stats">
<a href="#a1a1b6c48a9d8310804e0e666a6af78553f682f8" style="color: #1068bf;">
bcbio/ngsalign/bowtie2.py
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<li class="file-stats">
<a href="#50ebb36fdcbd533cf9fee8ba2898f9f470ccab88" style="color: #1068bf;">
bcbio/ngsalign/tophat.py
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<li class="file-stats">
<a href="#6ddf01621fd401f9c87acea171fc110bf3c7885c" style="color: #1068bf;">
bcbio/pipeline/config_utils.py
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<li class="file-stats">
<a href="#28669a7ddccdf8ac47c577727840379bba16c871" style="color: #1068bf;">
bcbio/pipeline/rnaseq.py
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<li class="file-stats">
<a href="#4529c40caf2a26a49dd0e781055543aaecdd79fc" style="color: #1068bf;">
bcbio/provenance/programs.py
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<a href="#60c9503c16c39a2c9a9b5d0272611f52d6fea731" style="color: #1068bf;">
bcbio/qc/qualimap.py
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<a href="#1632995720dec2c83890f793045a09678042e862" style="color: #1068bf;">
bcbio/qc/viral.py
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<a href="#6270e912e55ff9c93038ac7341b3a29df00cc7a1" style="color: #1068bf;">
bcbio/rnaseq/bcbiornaseq.py
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<li class="file-stats">
<a href="#5bf0ec075f9bd98bfd08ac77d0ffa18563a27ad8" style="color: #1068bf;">
bcbio/rnaseq/cufflinks.py
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<li class="file-stats">
<a href="#e0419363c1907d87150e8302779e144777a79539" style="color: #1068bf;">
bcbio/rnaseq/dexseq.py
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<li class="file-stats">
<a href="#3ece592962c93e563a8e8c319da752278663348e" style="color: #1068bf;">
bcbio/rnaseq/featureCounts.py
</a>
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<li class="file-stats">
<a href="#c01e86d4cab1a3dbb0f6b943a9202c6d94995bb0" style="color: #1068bf;">
bcbio/rnaseq/sailfish.py
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</li>
<li class="file-stats">
<a href="#0287de35830dbdcc13313ba0df6b5ba5e4cb9ab7" style="color: #1068bf;">
bcbio/rnaseq/salmon.py
</a>
</li>
<li class="file-stats">
<a href="#2cdd8023262242abfabb1ee24e7fd1e1cbb2562a" style="color: #1068bf;">
bcbio/structural/purecn.py
</a>
</li>
<li class="file-stats">
<a href="#ef9e027c453496e438d979be5491259d5e843de0" style="color: #1068bf;">
bcbio/utils.py
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</li>
<li class="file-stats">
<a href="#b7e501c752cdb46dea3a09628c724f2111008fc6" style="color: #1068bf;">
bcbio/variation/annotation.py
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<li class="file-stats">
<a href="#21ffe30f3c182af7db61c4a9b2d3c9f2012144b0" style="color: #1068bf;">
bcbio/variation/damage.py
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">The diff was not included because it is too large.</h5>
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<p style="font-size: small; color: #666;">
—
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