Collect metrics from a RNAseq BAM file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, strandedness:true ]
bam
:file
BAM/SAM file
*.{bam,sam}
ref_flat
Genome ref_flat file
fasta
Genome fasta file
rrna_intervals
Interval file of ribosomal RNA regions
metrics
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.rna_metrics
RNA alignment metrics files generated by picard
pdf
*.pdf
Plot normalized position vs. coverage in a pdf file generated by picard
versions_picard
${task.process}
:string
The process the versions were collected from
picard
The tool name
picard CollectRnaSeqMetrics --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.
