This module is used to clip primer sequences from your alignments.
meta
:map
Groovy Map containing sample information [ id:'sample1']
[ id:'sample1']
bam
:file
Sorted BAM file
*.bam
bai
BAI index of the input BAM file
*.bam.bai
bedpe
BEDPE file of primer pair locations
*.bed
*.primerclipped.bam
Sorted BAM file containing clipped query sequences according to the given primer pair locations
*.primerclipped.bam.bai
BAI index of the output BAM file
versions_bamclipper
${task.process}
:string
The name of the process
bamclipper
The name of the tool
1.0.0
The hardcoded version of the tool
versions_samtools
samtools
samtools version | sed '1!d;s/.* //'
:eval
The expression to obtain the version of the tool
versions
BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing
