Subworkflow: genome nexus - vcf2maf + annotationpipeline #58
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buehlere
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Mar 22, 2024
…-omics-workflows/modules into feature/genome_nexus_final avoiding merge conflicts
buehlere
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Apr 16, 2024
buehlere
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May 7, 2024
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@rnaidu a new general note is that we'd like to switch to using this version of vcf2maf: https://github.com/genome-nexus/vcf2maf-lite. Let me know if I can help.
…branch. subworkflow will be built off of here
buehlere
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Jun 26, 2024
nikhil
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Jun 26, 2024
| - "genomenexus": | ||
| description: "DSL2 module to perform an annotation of MAF file type using the genomenexus suite of conversion and annotation tools." | ||
| homepage: "https://github.com/genome-nexus/genome-nexus-annotation-pipeline/" | ||
| documentation: "https://github.com/genome-nexus/.github/blob/main/profile/README.md" |
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I would update the description. The tool itself (genomenexus) is not a nextflow dsl2 module its just a java pipeline.
Also: you can maybe use this for the docs (https://docs.genomenexus.org/)
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buehlere
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nikhil
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rhshah
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Jul 11, 2024
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| genomenexus: 'annotation pipeline version 1.0.3' |
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@rnaidu i know this is merged by we would need to update these versions
rhshah
reviewed
Jul 11, 2024
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| genomenexus: 'annotation pipeline version 1.0.3' |
rhshah
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Jul 11, 2024
| label 'process_low' | ||
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| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'ghcr.io/msk-access/genomenexus:vcf2maf_lite': |
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@rnaidu Also for both containers, is genome nexus team not hosting them?
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Genome Nexus VCF2MAF module + tests (tested locally and with nf-core data)
to be used in SNPs/indels nextflow workflow
PR checklist
versions.ymlfile.label