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strict syntax compatibility #130

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strict syntax compatibility #130

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3d4d23f
strict syntax compatibility
nvnieuwk Mar 5, 2026
fd489a3
fix issue with samtools faidx
nvnieuwk Mar 16, 2026
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1 change: 0 additions & 1 deletion .github/workflows/nf-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,6 @@ jobs:
- name: Run nf-test
id: run_nf_test
uses: ./.github/actions/nf-test
continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
env:
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
NXF_VERSION: ${{ matrix.NXF_VER }}
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13 changes: 5 additions & 8 deletions main.nf
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Expand Up @@ -154,16 +154,14 @@ output {
}
sample_vcfs {
path { meta, vcf, tbi ->
def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
vcf >> "${base}.vcf.gz"
tbi >> "${base}.vcf.gz.tbi"
vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
}
}
family_vcfs {
path { meta, vcf, tbi ->
def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
vcf >> "${base}.vcf.gz"
tbi >> "${base}.vcf.gz.tbi"
vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
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@matthdsm matthdsm Mar 5, 2026

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Parentheses?

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@nvnieuwk nvnieuwk Mar 5, 2026

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it's not needed as all logic happens in a string interpolation

tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
}
}
qdnaseq_out {
Expand All @@ -186,8 +184,7 @@ output {
}
bedpe {
path { meta, bedpe ->
def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
bedpe >> "${base}.bedpe"
bedpe >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".bedpe"
}
}
multiqc {
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