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fixed unaligned output

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kevinmenden 2020-12-18 09:20:35 +01:00
parent 1c89c9717b
commit 0eb20c14bf
1 changed files with 1 additions and 3 deletions
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4
software/bowtie/align/main.nf
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@ -27,12 +27,11 @@ process BOWTIE_ALIGN {
tuple val(meta), path('*.out'), emit: log tuple val(meta), path('*.out'), emit: log
path '*.version.txt' , emit: version path '*.version.txt' , emit: version
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
path 'test.txt', emit: test
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped" : '' def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
""" """
INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'` INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
@ -47,7 +46,6 @@ process BOWTIE_ALIGN {
2> ${prefix}.out \\ 2> ${prefix}.out \\
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam - | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
touch test.txt
if [ -f ${prefix}.unmapped.fastq ]; then if [ -f ${prefix}.unmapped.fastq ]; then
gzip ${prefix}.unmapped.fastq gzip ${prefix}.unmapped.fastq
fi fi