Locate and tag duplicate reads in a BAM file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Sequence reads file, can be SAM/BAM/CRAM format
*.{bam,cram,sam}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome fasta file, required for CRAM input
*.{fasta,fa}
meta3{:bash}
fai{:bash}
Reference genome fasta index
*.{fai}
bam{:bash}
*.bam{:bash}
BAM file with duplicate reads marked/removed
*.{bam}
bai{:bash}
*.bai{:bash}
An optional BAM index file. If desired, —CREATE_INDEX must be passed as a flag
*.{bai}
cram{:bash}
*.cram{:bash}
Output CRAM file
*.{cram}
metrics{:bash}
*.metrics.txt{:bash}
Duplicate metrics file generated by picard
*.{metrics.txt}
versions_picard{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
picard{:bash}
The tool name
picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'{:bash}
The command used to generate the version of the tool
versions{:bash}
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
