This module is used to clip primer sequences from your alignments.
meta{:bash}
:map
Groovy Map containing sample information [ id:'sample1']
[ id:'sample1']
bam{:bash}
:file
Sorted BAM file
*.bam
bai{:bash}
BAI index of the input BAM file
*.bam.bai
bedpe{:bash}
BEDPE file of primer pair locations
*.bed
*.primerclipped.bam{:bash}
Sorted BAM file containing clipped query sequences according to the given primer pair locations
*.primerclipped.bam
*.primerclipped.bam.bai{:bash}
BAI index of the output BAM file
*.primerclipped.bam.bai
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing
