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Standardise parameters (no tests yet until realigntarget creator ready)
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2 changed files with 15 additions and 6 deletions
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@ -9,20 +9,20 @@ process GATK_INDELREALIGNER {
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input:
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tuple val(meta), path(input), path(index), path(intervals)
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path path(fasta)
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path(fasta)
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path(fai)
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path(dict)
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path(known_vcf)
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output:
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tuple val(meta), path("*.bam"), emit: bam
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tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
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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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script:
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if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def known = known_vcf ? "-known ${known_vcf}" : ""
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@ -36,10 +36,11 @@ process GATK_INDELREALIGNER {
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"""
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gatk3 \\
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-Xmx${avail_mem}g \\
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-T IndelRealigner \\
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-R ${fasta} \\
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-nt ${task.cpus}
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-I ${bam} \\
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-I ${input} \\
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-targetIntervals ${intervals} \\
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${known} \\
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-o ${prefix}.bam \\
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@ -19,11 +19,11 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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- input:
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type: file
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description: Sorted and indexed BAM/CRAM/SAM file
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pattern: "*.bam"
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- bai:
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- index:
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type: file
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description: BAM index file
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pattern: "*.bai"
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@ -35,6 +35,14 @@ input:
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type: file
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description: Reference file used to generate BAM file
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pattern: ".{fasta,fa,fna}"
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- fai:
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type: file
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description: Index of reference file used to generate BAM file
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pattern: ".fai"
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- dict:
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type: file
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description: GATK dict file for reference
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pattern: ".dict"
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- known_vcf:
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type: file
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description: Optional input VCF file(s) with known indels
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