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bam_variant_calling_freebayes

8

A generic version of the freebayes subworkflow that can be imported to replace steps in [sarek](https://github.com/nf-core/sarek/blob/dev/subworkflows/nf-core/variantcalling/freebayes/main.nf) and [mag](https://github.com/nf-core/mag/blob/dev/subworkflows/local/ancient_dna.nf) Modules included: - SAMTOOLS_FAIDX - FREEBAYES - BCFTOOLS_SORT - BCFTOOLS_INDEX ## PR...

priyanka-surana

edmundmiller

### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

vmikk

### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

scorreard

### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an open PR for this? - [X] I have searched...

toniher

Leehom fix of cardinality

1

## PR checklist Contributes to #2154 - cardinality was wrong for the test, have changed this, and run nf-core modules test, and there are no failed jobs.

chriswyatt1

A generic version of the freebayes subworkflow that can be imported to replace steps in [sarek](https://github.com/nf-core/sarek/blob/dev/subworkflows/nf-core/variantcalling/freebayes/main.nf) and [mag](https://github.com/nf-core/mag/blob/dev/subworkflows/local/ancient_dna.nf) Modules included: - SAMTOOLS_FAIDX - FREEBAYES - BCFTOOLS_SORT - BCFTOOLS_INDEX

priyanka-surana

scorreard

maxulysse

Port sarek subworkflows to nf-core/modules

2

Please convert each of this as an issue when you start working on one. (That can be done by clicking on the circle dot `⊙` at the end of the...

maxulysse