[med-svn] [Git][med-team/bcbio][master] 3 commits: New upstream version 1.1.9

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
f8a1a562 by Steffen Möller at 2019-12-11T10:15:36Z
New upstream version 1.1.9
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1396015f by Steffen Möller at 2019-12-11T10:16:12Z
Update upstream source from tag 'upstream/1.1.9'

Update to upstream version '1.1.9'
with Debian dir 1c04d3ef7455100580dc4c5f1870b80f25082d30
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39e67630 by Steffen Möller at 2019-12-11T14:06:47Z
New upstream version - sadly few changes on our side

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30 changed files:

- HISTORY.md
- bcbio/bam/__init__.py
- bcbio/broad/picardrun.py
- bcbio/chipseq/__init__.py
- + bcbio/chipseq/atac.py
- bcbio/chipseq/macs2.py
- bcbio/chipseq/peaks.py
- bcbio/heterogeneity/chromhacks.py
- bcbio/ngsalign/bwa.py
- bcbio/ngsalign/star.py
- bcbio/pipeline/rnaseq.py
- bcbio/pipeline/run_info.py
- bcbio/pipeline/sample.py
- bcbio/qc/multiqc.py
- bcbio/qc/viral.py
- bcbio/upload/__init__.py
- bcbio/variation/effects.py
- debian/TODO
- debian/changelog
- debian/rules
- docs/contents/configuration.rst
- docs/contents/internals.rst
- docs/contents/outputs.rst
- requirements-conda.txt
- requirements.txt
- scripts/bcbio_setup_genome.py
- setup.py
- + tests/data/atac/atac_1.fq
- + tests/data/atac/atac_2.fq
- + tests/data/automated/run_info-atacseq.yaml


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/3db580be7b9324fe40b34003966f7ecdcf1402e0...39e6763084c5cccc0439e05924ea68ea9eccdeef

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/3db580be7b9324fe40b34003966f7ecdcf1402e0...39e6763084c5cccc0439e05924ea68ea9eccdeef
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