[med-svn] [Git][med-team/bcbio][master] 6 commits: routine-update: New upstream version

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
f7d5035e by Steffen Moeller at 2020-09-26T00:55:45+02:00
routine-update: New upstream version

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74736a56 by Steffen Moeller at 2020-09-26T00:55:46+02:00
New upstream version 1.2.4
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8fba113e by Steffen Moeller at 2020-09-26T00:56:22+02:00
Update upstream source from tag 'upstream/1.2.4'

Update to upstream version '1.2.4'
with Debian dir c51ab52b913b36889dab392d138d72164676f509
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e468bb0c by Steffen Moeller at 2020-09-26T00:56:22+02:00
routine-update: debhelper-compat 13

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f7c34366 by Steffen Moeller at 2020-09-26T00:56:29+02:00
Remove duplicate line from changelog.

Changes-By: lintian-brush

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e2bb5d97 by Steffen Moeller at 2020-09-26T00:59:14+02:00
New upstream version, adjusting picard->libpicard-java

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30 changed files:

- .github/ISSUE_TEMPLATE/bug_report.md
- .gitignore
- .travis.yml
- HISTORY.md
- README.md
- scripts/vm/Vagrantfile → Vagrantfile
- bcbio/bam/__init__.py
- bcbio/bam/fastq.py
- bcbio/chipseq/__init__.py
- bcbio/chipseq/atac.py
- bcbio/chipseq/peaks.py
- bcbio/cwl/create.py
- + bcbio/data/umis/qiaseq-upx-384-cb1.txt.gz
- + bcbio/data/umis/qiaseq-upx-384-transform.json
- + bcbio/data/umis/qiaseq-upx-96-cb1.txt.gz
- + bcbio/data/umis/qiaseq-upx-96-transform.json
- bcbio/distributed/ipythontasks.py
- bcbio/distributed/multitasks.py
- bcbio/heterogeneity/chromhacks.py
- bcbio/hla/optitype.py
- bcbio/install.py
- bcbio/ngsalign/bismark.py
- bcbio/ngsalign/bwa.py
- bcbio/ngsalign/star.py
- bcbio/pipeline/alignment.py
- bcbio/pipeline/datadict.py
- bcbio/pipeline/main.py
- bcbio/pipeline/qcsummary.py
- bcbio/pipeline/sample.py
- bcbio/qc/atac.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/915f9844da6f8643b8f2bc9923dba096659eb08c...e2bb5d97d9ca2d0c2e677270061eabf692b048e1

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/915f9844da6f8643b8f2bc9923dba096659eb08c...e2bb5d97d9ca2d0c2e677270061eabf692b048e1
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