nf-core/picard/collectrnaseqmetrics @ 0.0.0-0c7146d
Summary
Collect metrics from a RNAseq BAM file
Get started
Add the following snippet to your workflow script to include this module.
include { PICARD_COLLECTRNASEQMETRICS } from 'nf-core/picard/collectrnaseqmetrics'
License
MIT License
Process
Name
|
PICARD_COLLECTRNASEQMETRICS |
|---|
Input
4 channels
#1
tuple
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
file
|
Genome ref_flat file |
|---|
fasta
file
|
Genome fasta file |
|---|
rrna_intervals
file
|
Interval file of ribosomal RNA regions |
|---|
Output
3 channels
#1
pdf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.pdf
file
|
Plot normalized position vs. coverage in a pdf file generated by picard |
#2
metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.rna_metrics
file
|
RNA alignment metrics files generated by picard *.rna_metrics
|
#3
versions_picard
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
picard
string
|
The tool name |
picard CollectRnaSeqMetrics --version 2>&1 | sed -n 's/.*Version://p'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| picard | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | https://broadinstitute.github.io/picard/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:02:33 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectrnaseqmetrics/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/collectrnaseqmetrics/blobs/sha256:fd82fd477fb6db1d04a644c982cad503af067a6bdad48f99c5ccab835df8edb9 |
| Size | 3.2 KB |
| Checksum | sha256:fd82fd477fb6db1d04a644c982cad503af067a6bdad48f99c5ccab835df8edb9 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:02:33 (UTC) | 1 | 3.2 KB | - |