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Fix CI: Remove oncokb_genes file dependency and use process substitution #1052

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Merged
gongyixiao merged 3 commits into from
Feb 6, 2026
Merged

Fix CI: Remove oncokb_genes file dependency and use process substitution #1052

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fce863d
Fix CI: Remove oncokb_genes file dependency and use process substitution
gongyixiao Feb 5, 2026
98ac093
Fix CI: Replace process substitution with concise command substitutio…
gongyixiao Feb 5, 2026
ebebcfa
Update CI workflow to use Ubuntu 24.04
gongyixiao Feb 5, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ on:

jobs:
test:
runs-on: ubuntu-22.04
runs-on: ubuntu-24.04
env:
NXF_VER: "25.04.7"

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3 changes: 1 addition & 2 deletions modules/process/SNV/SomaticAnnotateMaf.nf
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Expand Up @@ -6,7 +6,6 @@ process SomaticAnnotateMaf {
input:
tuple val(idTumor), val(idNormal), val(target), path(vcfMerged)
tuple path(genomeFile), path(genomeIndex), path(genomeDict), path(vepCache), path(isoforms)
path(oncokb_genes) // used for test, test_singularity profile only

output:
tuple val(idTumor), val(idNormal), val(target), path("${outputPrefix}.maf"), emit: mafFile
Expand Down Expand Up @@ -66,6 +65,6 @@ process SomaticAnnotateMaf {
--normal-panel-count ${params.somaticVariant.ponCount} \
--maf-file ${outputPrefix}.raw.oncokb.maf \
--output-prefix ${outputPrefix} \
--onco "${["test","test_singularity"].contains(workflow.profile) ? oncokb_genes : "https://data-legacy.oncokb.aws.mskcc.org/api/v1/genes/" }"
--onco ${["test","test_singularity"].contains(workflow.profile) ? "\$(echo '[]' > empty.json && echo empty.json)" : "'https://data-legacy.oncokb.aws.mskcc.org/api/v1/genes/'" }
"""
}
6 changes: 1 addition & 5 deletions modules/subworkflow/snv_wf.nf
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Expand Up @@ -69,11 +69,7 @@ workflow snv_wf

SomaticAnnotateMaf(SomaticCombineChannel.out.mutationMergedVcf,
Channel.value([referenceMap.genomeFile, referenceMap.genomeIndex, referenceMap.genomeDict,
referenceMap.vepCache, referenceMap.isoforms]),
["test","test_singularity"].contains(workflow.profile) ?
Channel.value([file(workflow.projectDir + "/containers/vcf2maf/oncokb_genes.json")]) :
Channel.value([])
)
referenceMap.vepCache, referenceMap.isoforms]))


hlaOutput.combine(SomaticAnnotateMaf.out.mafFile, by: [1,2]).set{ input4Neoantigen }
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