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feat: added STAR temp dir #453
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johanneskoester
approved these changes
Feb 21, 2022
@fgvieira thanks a lot for all this updating and improving! I've made you a maintainer now, so that you can also merge and review PRs yourself if you want. |
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Description
Add a temp dir and made output file names more flexible. Now, all of STAR output is saved to a temp dir and only those files specified as outputs by the user are copied over to the final location
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,