diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml index ab68274eb89..ed1e5e9efed 100644 --- a/modules/nf-core/shapeit5/ligate/meta.yml +++ b/modules/nf-core/shapeit5/ligate/meta.yml @@ -12,8 +12,8 @@ tools: homepage: "https://odelaneau.github.io/shapeit5/" documentation: "https://odelaneau.github.io/shapeit5/docs/documentation" tool_dev_url: "https://github.com/odelaneau/shapeit5" - doi: "10.1101/2022.10.19.512867 " - licence: "['MIT']" + doi: "10.1101/2022.10.19.512867" + licence: ["MIT"] input: - meta: type: map diff --git a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf index 0ddebcb3d41..966f9019055 100644 --- a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf +++ b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf @@ -66,10 +66,9 @@ workflow VCF_PHASE_SHAPEIT5 { ch_ligate_input = SHAPEIT5_PHASECOMMON.out.phased_variant .join(VCF_INDEX1.out.csi, failOnMismatch:true, failOnDuplicate:true) - .view() .map{ meta, vcf, csi -> newmeta = meta + [id: meta.id.split("_")[0..-2].join("_")] - [newmeta, vcf, csi]}.view() + [newmeta, vcf, csi]} .combine(ch_chunks_number, by:0) .map{meta, vcf, csi, chunks_num -> [groupKey(meta, chunks_num), vcf, csi]} diff --git a/tests/modules/nf-core/shapeit5/ligate/main.nf b/tests/modules/nf-core/shapeit5/ligate/main.nf index 3b92a03ed8f..1213f7bd3a8 100644 --- a/tests/modules/nf-core/shapeit5/ligate/main.nf +++ b/tests/modules/nf-core/shapeit5/ligate/main.nf @@ -32,7 +32,7 @@ workflow test_shapeit5_ligate { phase_input = Channel.of([[ id:'NA12878_1X']]) .combine(BCFTOOLS_VIEW.out.vcf.collect().map{it[1]}) .combine(BCFTOOLS_INDEX.out.csi.collect().map{it[1]}) - .combine(sample).view() + .combine(sample) .combine(region) .map{ meta, vcf, csi, sample, region -> [meta + [region: region.replace(":","_")], @@ -43,7 +43,6 @@ workflow test_shapeit5_ligate { phased_variant = SHAPEIT5_PHASECOMMON.output.phased_variant .map{ meta, vcf -> [meta.subMap(["id"]), vcf]} - .view() BCFTOOLS_INDEX2 ( phased_variant ) @@ -55,6 +54,5 @@ workflow test_shapeit5_ligate { a.getName() <=> b.getName()}, csi]} - ligate_input.view() SHAPEIT5_LIGATE ( ligate_input ) } diff --git a/tests/modules/nf-core/shapeit5/ligate/nextflow.config b/tests/modules/nf-core/shapeit5/ligate/nextflow.config index 665b5b02e5f..f96da6737f4 100644 --- a/tests/modules/nf-core/shapeit5/ligate/nextflow.config +++ b/tests/modules/nf-core/shapeit5/ligate/nextflow.config @@ -1,6 +1,7 @@ process { withName: BCFTOOLS_VIEW { ext.args = [ + "-Oz", "-e 'GT=\"./.\"||GT=\".\"'" ].join(' ') ext.prefix = { "${meta.id}" } diff --git a/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config b/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config index 2d06b2b2718..9a9f10a640b 100644 --- a/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config +++ b/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config @@ -5,6 +5,7 @@ process { } withName: BCFTOOLS_VIEW { ext.args = [ + "-Oz", "-e 'GT=\"./.\"||GT=\".\"'" ].join(' ') }