Collect multiple metrics from a BAM file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
SAM/BAM/CRAM file
*.{sam,bam,cram}
bai{:bash}
Optional SAM/BAM/CRAM file index
*.{sai,bai,crai}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’]
fasta{:bash}
Genome fasta file
meta3{:bash}
fai{:bash}
Index of FASTA file. Only needed when fasta is supplied.
*.fai
metrics{:bash}
*_metrics{:bash}
Alignment metrics files generated by picard
*_{metrics}
pdf{:bash}
*.pdf{:bash}
PDF plots of metrics
*.{pdf}
versions{:bash}
versions.yml{:bash}
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.
