Fix bcftools stubs to behave like program #6666
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This PR fixes issues where the stubs doesn't behave like the program would.
I.e. running bcftools with
--output-type u/b --write-index=tbi
, it still outputs a csi index, but were outputting a tbi index in the stubs:--output-type v --write-index=tbi
- error--output-type v --write-index=csi
- error--output-type z --write-index=tbi
- tbi index--output-type z --write-index=csi
- csi index--output-type u --write-index=tbi
- csi index <- note--output-type u --write-index=csi
- csi index--output-type b --write-index=tbi
- csi index <- note--output-type b --write-index=csi
- csi indexIt takes the custom function added for bcftools csq in #6605, together with a similar function for the index, and applies it to the applicable modules.
PR checklist
Closes #XXX
versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda