Loading modules.json +1 −1 Original line number Diff line number Diff line Loading @@ -31,7 +31,7 @@ "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" }, "picard/markduplicates": { "git_sha": "c5235a983d454787fa0c3247b02086969217163b" "git_sha": "b2a6f5409efa6eb065c8186c606e68ff8004ba51" }, "samtools/flagstat": { "git_sha": "c5235a983d454787fa0c3247b02086969217163b" Loading modules/nf-core/modules/picard/markduplicates/main.nf +4 −3 Original line number Diff line number Diff line Loading @@ -23,6 +23,7 @@ process PICARD_MARKDUPLICATES { output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics.txt"), emit: metrics path "*.version.txt" , emit: version Loading @@ -40,9 +41,9 @@ process PICARD_MARKDUPLICATES { -Xmx${avail_mem}g \\ MarkDuplicates \\ $options.args \\ INPUT=$bam \\ OUTPUT=${prefix}.bam \\ METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt -I $bam \\ -O ${prefix}.bam \\ -M ${prefix}.MarkDuplicates.metrics.txt echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt """ Loading modules/nf-core/modules/picard/markduplicates/meta.yml +44 −39 Original line number Diff line number Diff line Loading @@ -34,6 +34,10 @@ output: type: file description: BAM file with duplicate reads marked/removed pattern: "*.{bam}" - bai: type: file description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag pattern: "*.{bai}" - metrics: type: file description: Duplicate metrics file generated by picard Loading @@ -44,3 +48,4 @@ output: pattern: "*.{version.txt}" authors: - "@drpatelh" - "@projectoriented" Loading
modules.json +1 −1 Original line number Diff line number Diff line Loading @@ -31,7 +31,7 @@ "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d" }, "picard/markduplicates": { "git_sha": "c5235a983d454787fa0c3247b02086969217163b" "git_sha": "b2a6f5409efa6eb065c8186c606e68ff8004ba51" }, "samtools/flagstat": { "git_sha": "c5235a983d454787fa0c3247b02086969217163b" Loading
modules/nf-core/modules/picard/markduplicates/main.nf +4 −3 Original line number Diff line number Diff line Loading @@ -23,6 +23,7 @@ process PICARD_MARKDUPLICATES { output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics.txt"), emit: metrics path "*.version.txt" , emit: version Loading @@ -40,9 +41,9 @@ process PICARD_MARKDUPLICATES { -Xmx${avail_mem}g \\ MarkDuplicates \\ $options.args \\ INPUT=$bam \\ OUTPUT=${prefix}.bam \\ METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt -I $bam \\ -O ${prefix}.bam \\ -M ${prefix}.MarkDuplicates.metrics.txt echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt """ Loading
modules/nf-core/modules/picard/markduplicates/meta.yml +44 −39 Original line number Diff line number Diff line Loading @@ -34,6 +34,10 @@ output: type: file description: BAM file with duplicate reads marked/removed pattern: "*.{bam}" - bai: type: file description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag pattern: "*.{bai}" - metrics: type: file description: Duplicate metrics file generated by picard Loading @@ -44,3 +48,4 @@ output: pattern: "*.{version.txt}" authors: - "@drpatelh" - "@projectoriented"
