Collect multiple metrics from a BAM file
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
SAM/BAM/CRAM file
*.{sam,bam,cram}
bai:file
Optional SAM/BAM/CRAM file index
*.{sai,bai,crai}
meta2:map
Groovy Map containing reference information e.g. [ id:‘genome’]
fasta:file
Genome fasta file
meta3:map
fai:file
Index of FASTA file. Only needed when fasta is supplied.
*.fai
metrics
*_metrics:file
Alignment metrics files generated by picard
*_{metrics}
pdf
*.pdf:file
PDF plots of metrics
*.{pdf}
versions
versions.yml:file
File containing software versions
versions.yml
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
