mark duplicate alignments in a coordinate sorted file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference genome file
*.{fa,fasta}
fai
Reference genome index file
*.fai
bam
*.bam
BAM file
*{.bam}
cram
*.cram
CRAM file
*{.cram}
sam
*.sam
SAM file
*{.sam}
versions_samtools
${task.process}
:string
The process the versions were collected from
samtools
The tool name
samtools version | sed '1!d;s/.* //'
The command used to generate the version of the tool
versions
Tools for dealing with SAM, BAM and CRAM files
