Locate and tag duplicate reads in a BAM file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM file
*.{bam,cram}
*.bam{:bash}
BAM file with duplicate reads marked/removed
*.{bam}
metrics{:bash}
*.metrics.txt{:bash}
Duplicate metrics file generated by biobambam
*.{metrics.txt}
versions_biobambam{:bash}
${task.process}{:bash}
:string
The name of the process
biobambam{:bash}
The name of the tool
bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\$//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
biobambam is a set of tools for early stage alignment file processing.
