From fce863d9c328227806a0967e56e82ff57dd40b5a Mon Sep 17 00:00:00 2001 From: YGong Date: Thu, 5 Feb 2026 13:57:12 -0500 Subject: [PATCH 1/3] Fix CI: Remove oncokb_genes file dependency and use process substitution --- modules/process/SNV/SomaticAnnotateMaf.nf | 3 +-- modules/subworkflow/snv_wf.nf | 6 +----- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/modules/process/SNV/SomaticAnnotateMaf.nf b/modules/process/SNV/SomaticAnnotateMaf.nf index e201dd05..81745d3b 100644 --- a/modules/process/SNV/SomaticAnnotateMaf.nf +++ b/modules/process/SNV/SomaticAnnotateMaf.nf @@ -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 @@ -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 '[]')" : "'https://data-legacy.oncokb.aws.mskcc.org/api/v1/genes/'" } """ } diff --git a/modules/subworkflow/snv_wf.nf b/modules/subworkflow/snv_wf.nf index 935246b7..a22d574b 100644 --- a/modules/subworkflow/snv_wf.nf +++ b/modules/subworkflow/snv_wf.nf @@ -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 } From 98ac09367b9f1e8b417e882b9b5c0f8b5f0433fa Mon Sep 17 00:00:00 2001 From: YGong Date: Thu, 5 Feb 2026 15:25:02 -0500 Subject: [PATCH 2/3] Fix CI: Replace process substitution with concise command substitution logic (using empty.json) --- modules/process/SNV/SomaticAnnotateMaf.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/process/SNV/SomaticAnnotateMaf.nf b/modules/process/SNV/SomaticAnnotateMaf.nf index 81745d3b..abaa6731 100644 --- a/modules/process/SNV/SomaticAnnotateMaf.nf +++ b/modules/process/SNV/SomaticAnnotateMaf.nf @@ -65,6 +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) ? "<(echo '[]')" : "'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/'" } """ } From ebebcfac964b72c9e66418b724e314737fdf979b Mon Sep 17 00:00:00 2001 From: gongyixiao <5620765+gongyixiao@users.noreply.github.com> Date: Thu, 5 Feb 2026 16:34:58 -0500 Subject: [PATCH 3/3] Update CI workflow to use Ubuntu 24.04 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 11b05e92..934dfabc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,7 +9,7 @@ on: jobs: test: - runs-on: ubuntu-22.04 + runs-on: ubuntu-24.04 env: NXF_VER: "25.04.7"