nf-core/picard/collectalignmentsummarymetrics @ 0.0.0-0c7146d
Summary
Collect metrics about the alignment summary of a paired-end library.
Get started
Add the following snippet to your workflow script to include this module.
include { PICARD_COLLECTALIGNMENTSUMMARYMETRICS } from 'nf-core/picard/collectalignmentsummarymetrics'
License
MIT License
Process
Name
|
PICARD_COLLECTALIGNMENTSUMMARYMETRICS |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Fasta file *.{fasta}
|
Output
2 channels
#1
metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Standard alignment summary metrics *.txt
|
#2
versions_picard
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
picard
string
|
The tool name |
picard CollectAlignmentSummaryMetrics --version 2>&1 | sed -n 's/.*Version://p'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| picard | Java tools for working with NGS data in the BAM format | https://broadinstitute.github.io/picard/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:02:26 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectalignmentsummarymetrics/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/collectalignmentsummarymetrics/blobs/sha256:446e11c6efa92b6e4f308da7382eeaa810673514dd1036f6fb57ef979e624db5 |
| Size | 3.2 KB |
| Checksum | sha256:446e11c6efa92b6e4f308da7382eeaa810673514dd1036f6fb57ef979e624db5 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:02:26 (UTC) | 1 | 3.2 KB | - |