Collect multiple metrics from a BAM file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
SAM/BAM/CRAM file
*.{sam,bam,cram}
bai
Optional SAM/BAM/CRAM file index
*.{sai,bai,crai}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’]
fasta
Genome fasta file
meta3
fai
Index of FASTA file. Only needed when fasta is supplied.
*.fai
metrics
*_metrics
Alignment metrics files generated by picard
*_{metrics}
pdf
*.pdf
PDF plots of metrics
*.{pdf}
versions_picard
${task.process}
:string
The process the versions were collected from
picard
The tool name
picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'
The command used to generate the version of the tool
versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
