add process and config for vcf2maf #15
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scwatts
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Aug 28, 2025
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Considering reverting if for nothing other than consistency
scwatts
reviewed
Aug 28, 2025
modules/local/vcf2maf/main.nf
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| vcf2maf: 1.6.22 |
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Let's switch this to the standard 'no version' template
scwatts
reviewed
Aug 28, 2025
modules/local/vcf2maf/main.nf
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| tag "${meta.id}" | ||
| label 'process_medium' | ||
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| container 'docker.io/qclayssen/vcf2maf:debian_v1.6.22' |
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To be pushed the UMCCR account as you mentioned
scwatts
reviewed
Aug 28, 2025
scwatts
reviewed
Aug 28, 2025
conf/refdata.config
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| } | ||
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| genome { | ||
| build = 'GRCh38' |
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The genome block is reserved for filepaths and since we'll only use GRCh38 with sash in the foreseeable future, I would remove this and hardcode the value into the corresponding argument in the VCF2MAF process
scwatts
reviewed
Aug 28, 2025
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Request from Sehrish slack