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