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feat: added wrapper-utils, and tempdirs #467
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fgvieira
changed the title
Added wrapper-utils, and tempdirs
feat: added wrapper-utils, and tempdirs
Mar 20, 2022
Hey @fgvieira any chance to get this ready for merging? If we wait too long with this, conflicts will accumulate as it touches many wrappers. |
I'm waiting on a PR on |
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johanneskoester
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Aug 16, 2022
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Description
Added
snakemake-wrapper-utils
and temp dirs (withtempfile
).Also updated some docs.
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,