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feat: Add wrapper for GATK DepthOfCoverage #494
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johanneskoester
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snakemake:master
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Genomic-Medicine-Linkoping:gatk-depth-of-coverage
Sep 19, 2022
Merged
feat: Add wrapper for GATK DepthOfCoverage #494
johanneskoester
merged 25 commits into
snakemake:master
from
Genomic-Medicine-Linkoping:gatk-depth-of-coverage
Sep 19, 2022
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fgvieira
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Jun 13, 2022
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
…edicine-Linkoping/snakemake-wrappers into gatk-depth-of-coverage
johanneskoester
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Jun 14, 2022
fgvieira
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Jun 17, 2022
Smeds
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Jun 29, 2022
Co-authored-by: Patrik Smeds <patrik.smeds@gmail.com>
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johanneskoester
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Aug 16, 2022
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
fgvieira
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Aug 18, 2022
@johanneskoester Should there be done anything additional so that this PR can be merged? |
johanneskoester
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Sep 19, 2022
Thanks a lot! |
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Jan 10, 2023
* feat: add depthofcoverage wrapper * test: add test and test data for depthofcoverage * docs: add comments describing some of the input and output fields * docs: add link to the tool documentation * docs: add comment * feat: add wildcards for sample names * fix: update bio/gatk/depthofcoverage/meta.yaml Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com> * fix: add missing wildcard expression * feat: remove multi-sample processing * feat: name all generated output files explicitly * fix: remove "--use-conda" Co-authored-by: Patrik Smeds <patrik.smeds@gmail.com> * refactor: simplify getting output file basename * fix: update channel priority order Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com> Co-authored-by: Patrik Smeds <patrik.smeds@gmail.com> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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Description
This PR adds a wrapper for GATK DepthOfCoverage tool.
QC
For all wrappers added by this PR, I made sure that
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,