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@ -12,10 +12,13 @@ process SAMTOOLS_VIEW {
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path fasta
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output:
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tuple val(meta), path("*.bam") , emit: bam , optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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tuple val(meta), path("*.sam") , emit: sam , optional: true
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.bam"), emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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tuple val(meta), path("*.sam"), emit: sam, optional: true
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tuple val(meta), path("*.bai"), emit: bai, optional: true
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tuple val(meta), path("*.csi"), emit: csi, optional: true
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tuple val(meta), path("*.crai"), emit: crai, optional: true
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -35,8 +38,8 @@ process SAMTOOLS_VIEW {
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--threads ${task.cpus-1} \\
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${reference} \\
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$args \\
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$input \\
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> ${prefix}.${file_type}
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-o ${prefix}.${file_type} \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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