Parallel sorting and duplicate marking
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bams{:bash}
:file
List containing 1 or more bam files
meta2{:bash}
Groovy Map containing genome information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome in FASTA format (optional)
*.{fa,fasta,fna}
fai{:bash}
Reference genome in FASTA index format (optional)
*.{fai}
bam{:bash}
*.bam{:bash}
BAM file with duplicate reads marked/removed
*.bam
bam_index{:bash}
*.bam.bai{:bash}
BAM index file
*.bai
cram{:bash}
*.cram{:bash}
CRAM file with duplicate reads marked/removed
*.cram
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
bamsormadup --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.
