[med-svn] [Git][med-team/bcbio][master] 7 commits: New upstream version 1.1.7

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
b50e6f19 by Steffen Möller at 2019-10-19T12:01:29Z
New upstream version 1.1.7
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dd4280b1 by Steffen Möller at 2019-10-19T12:02:04Z
Update upstream source from tag 'upstream/1.1.7'

Update to upstream version '1.1.7'
with Debian dir 687a566dcf2fc239ec1c51afd05eb2b1f6d5e08e
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1bfdb9f4 by Steffen Möller at 2019-10-19T12:04:23Z
Prepare for new upstream release.

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37c2bb77 by Steffen Möller at 2019-10-19T12:10:48Z
Directing bcbio to contrib

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fa26f197 by Steffen Möller at 2019-10-19T12:13:27Z
Avoid lintian errors because of missing -x flags

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5ff0ae1b by Steffen Möller at 2019-10-19T12:20:26Z
Added ref to conda

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c8f9eac5 by Steffen Möller at 2019-10-19T12:20:58Z
Merge branch 'master' of salsa.debian.org:med-team/bcbio

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30 changed files:

- + CODE_OF_CONDUCT.md
- HISTORY.md
- bcbio/bam/__init__.py
- bcbio/bam/coverage.py
- bcbio/bam/fastq.py
- bcbio/broad/__init__.py
- + bcbio/chipseq/antibodies.py
- bcbio/chipseq/macs2.py
- bcbio/distributed/ipythontasks.py
- bcbio/distributed/multitasks.py
- bcbio/distributed/runfn.py
- bcbio/heterogeneity/bubbletree.py
- bcbio/hla/optitype.py
- bcbio/illumina/flowcell.py
- bcbio/illumina/machine.py
- bcbio/install.py
- + bcbio/ngsalign/bismark.py
- + bcbio/ngsalign/bsmap.py
- bcbio/ngsalign/postalign.py
- bcbio/ngsalign/star.py
- bcbio/pipeline/alignment.py
- bcbio/pipeline/datadict.py
- bcbio/pipeline/main.py
- bcbio/pipeline/rnaseq.py
- bcbio/pipeline/run_info.py
- bcbio/pipeline/sample.py
- bcbio/pipeline/sra.py
- bcbio/provenance/programs.py
- bcbio/provenance/versioncheck.py
- bcbio/qc/chipseq.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/5429a03ecebe644d6cfbb1dd30c6c3cd58f53fc4...c8f9eac5127fe3bdaa65fb13c779509c9756d863

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/5429a03ecebe644d6cfbb1dd30c6c3cd58f53fc4...c8f9eac5127fe3bdaa65fb13c779509c9756d863
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