diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index d77a1c6..0c18ee7 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -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: ${{ matrix.NXF_VER }} diff --git a/main.nf b/main.nf index c8d77c7..32ee9fe 100644 --- a/main.nf +++ b/main.nf @@ -154,16 +154,14 @@ output { } sample_vcfs { path { meta, vcf, tbi -> - def base = "${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" + tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi" } } qdnaseq_out { @@ -186,8 +184,7 @@ output { } bedpe { path { meta, bedpe -> - def base = "${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 {