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Output log file for MultiQC

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drpatelh 2021-02-23 20:36:23 +00:00
parent 9098ba41c8
commit 89cd71309c
1 changed files with 4 additions and 2 deletions
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6
software/ivar/trim/main.nf
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@ -19,11 +19,12 @@ process IVAR_TRIM {
} }
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(bai)
path bed path bed
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path('*.log'), emit: log
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
@ -34,7 +35,8 @@ process IVAR_TRIM {
$options.args \\ $options.args \\
-i $bam \\ -i $bam \\
-b $bed \\ -b $bed \\
-p $prefix -p $prefix \\
> ${prefix}.ivar.log
ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
""" """