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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
6 stars 1 forks source link

Save a process, create index within the module #162

Closed matthdsm closed 7 months ago

matthdsm commented 7 months ago

bcftools concat supports the --write-index flag, so an extra tabix process is superfluous.

https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/blob/bddaca3e32e98535626053afe627bbb64852e36a/subworkflows/local/vcf_concat_bcftools/main.nf#L30-L35

nvnieuwk commented 7 months ago

This option creates .csi index files, which is not supported by all tools :cry:

matthdsm commented 7 months ago

NOOOOOooooooo....;