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luslab-umitools | Added index output from module
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3 changed files with 9 additions and 9 deletions
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@ -7,3 +7,4 @@ channels:
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- defaults
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dependencies:
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- umi_tools=1.0.1
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- samtools=1.1.0
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@ -17,7 +17,8 @@ process umitools_dedup {
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tuple val(sample_id), path(bam)
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output:
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tuple val(sample_id), path("*.dedup.bam"), emit: dedupBam
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tuple val(sample_id), path("${sample_id}.dedup.bam"), emit: dedupBam
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tuple val(sample_id), path("${sample_id}.dedup.bam.bai"), emit: dedupBai
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path "*.dedup.log", emit: report
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script:
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@ -32,15 +33,16 @@ process umitools_dedup {
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}
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// Contruct CL line
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command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
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dedup_command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
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// Log
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if (params.verbose){
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println ("[MODULE] umi_tools/dedup exec: " + command)
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println ("[MODULE] umi_tools/dedup command: " + dedup_command)
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}
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//SHELL
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"""
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${command}
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${dedup_command}
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samtools index ${sample_id}.dedup.bam
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"""
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}
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@ -24,12 +24,9 @@ processes:
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- sample_id:
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type: string
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description: Sample identifier
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- bai:
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type: file
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description: BAM file index
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- bam:
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type: file
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description: BAM sequence file
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type: file array
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description: BAM sequence file and associated BAI index file
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output:
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- dedupBam:
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type: tuple
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