fix: ensembl-variation - remove index #1760
Merged
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Description
This wrapper is currently failing when concatenating chromosomes.
That issue is caused by each chromosomal vcf having a separate index file only containing the corresponding chromosome itself.
If
csi
files are presentbcftools concat
checks the indexed contigs of each index file and expects them to be present in all of the other vcf headers.As chromosomes do not overlap it should be fine to drop indexes.
QC
For all wrappers added by this PR,
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,