[med-svn] [Git][med-team/bcbio][upstream] New upstream version 1.2.9

[Lance Lin (@linqigang)]

Lance Lin pushed to branch upstream at Debian Med / bcbio


Commits:
d053e607 by Lance Lin at 2022-08-17T20:08:13+07:00
New upstream version 1.2.9
- - - - -


30 changed files:

- .github/ISSUE_TEMPLATE/bug_report.md
- HISTORY.md
- bcbio/broad/__init__.py
- bcbio/broad/metrics.py
- bcbio/broad/picardrun.py
- bcbio/chipseq/macs2.py
- bcbio/chipseq/peaks.py
- + bcbio/data/umis/harvard-indrop-v31-cb1.txt.gz
- + bcbio/data/umis/harvard-indrop-v31-cb2.txt.gz
- + bcbio/data/umis/harvard-indrop-v31-transform.json
- bcbio/hla/optitype.py
- bcbio/install.py
- bcbio/ngsalign/bismark.py
- bcbio/ngsalign/bowtie2.py
- bcbio/ngsalign/tophat.py
- bcbio/pipeline/config_utils.py
- bcbio/pipeline/rnaseq.py
- bcbio/provenance/programs.py
- bcbio/qc/qualimap.py
- bcbio/qc/viral.py
- bcbio/rnaseq/bcbiornaseq.py
- bcbio/rnaseq/cufflinks.py
- bcbio/rnaseq/dexseq.py
- bcbio/rnaseq/featureCounts.py
- bcbio/rnaseq/sailfish.py
- bcbio/rnaseq/salmon.py
- bcbio/structural/purecn.py
- bcbio/utils.py
- bcbio/variation/annotation.py
- bcbio/variation/damage.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/d053e6078085c8673f1e08743ea44758f5d20ca4

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