[FEATURE] Make modules for: - Githubissues

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

https://nf-co.re/sarek

MIT License

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[FEATURE] Make modules for: #343

Closed maxulysse closed 3 years ago

maxulysse commented 3 years ago

We need modules in nf-core/modules for:

Please tick a module if you are working on one, and add the link to the PR once you created it

[ ] allelecounter
[ ] ascat
[x] bwa-mem2/index - https://github.com/nf-core/modules/pull/166
[x] bwa-mem2/mem - https://github.com/nf-core/modules/pull/166
[x] cnvkit - https://github.com/nf-core/modules/pull/173
[ ] controlfreec/freec
[ ] fgbio/callmolecularconsensusreads
[ ] fgbio/fastqtobam
[ ] fgbio/groupreadsbyumi
[ ] freebayes/single
[ ] freebayes/somatic
[ ] gatk/calculatecontamination
[ ] gatk/filtermutectcalls
[ ] gatk/getpileupsummaries
[ ] gatk/applybqsr
[ ] gatk/baserecalibrator
[x] gatk/createsequencedictionary https://github.com/nf-core/modules/pull/177
[ ] gatk/fastqtosam
[ ] gatk/gatherbqsrreports
[ ] gatk/genotypegvcf
[ ] gatk/haplotypecaller
[ ] gatk/markduplicates
[ ] gatk/mergemutectstats
[ ] gatk/mutect2
[x] manta/single
[ ] manta/single_tumor
[ ] manta/somatic
[x] msisensor/msi
[x] msisensor/scan
[x] qualimap/bamqc https://github.com/nf-core/modules/pull/129
[x] samtools/faidx https://github.com/nf-core/modules/pull/129
[ ] samtools/merge
[ ] snpeff
[ ] strelka/germline
[ ] strelka/somatic
[ ] strelka/somatic_bp
[x] tabix/bgzip https://github.com/nf-core/modules/pull/180
[x] tabix/tabix https://github.com/nf-core/modules/pull/179
[x] tiddit https://github.com/nf-core/modules/pull/252
[ ] vcftools
[ ] vep

maxulysse commented 3 years ago

All modules to be created now have separate issues in the nf-core/modules repo under the nf-core/sarek milestone