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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Kevin Menden 2020-12-18 08:16:18 +01:00 committed by GitHub
parent 57ab6dbcbf
commit 41329b8982
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2 changed files with 4 additions and 4 deletions
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4
software/bowtie/align/main.nf
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@ -25,7 +25,7 @@ process BOWTIE_ALIGN {
output: output:
tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.bam'), emit: bam
tuple val(meta), path('*.out'), emit: log tuple val(meta), path('*.out'), emit: log
path 'bowtie.version.txt', emit: version path '*.version.txt' , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
@ -45,6 +45,6 @@ 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 -
bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
""" """
} }

4
software/bowtie/index/main.nf
View file

@ -29,7 +29,7 @@ process BOWTIE_INDEX {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
""" """
mkdir bowtie mkdir bowtie
bowtie-build --threads $task.cpus ${fasta} bowtie/${fasta.baseName}.index bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
""" """
} }