Collect multiple metrics from a BAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
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
Alignment metrics files generated by picard
*_{metrics}
pdf
PDF plots of metrics
*.{pdf}
versions
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.