nf-core/picard/collectalignmentsummarymetrics @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:35:53 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectalignmentsummarymetrics/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/collectalignmentsummarymetrics/blobs/sha256:abcfc9f56f25a3dcf90f683e1174b7fa50e29e6e1e2810aafc5e7e20550eb6b7 |
| Size | 3.2 KB |
| Checksum | sha256:abcfc9f56f25a3dcf90f683e1174b7fa50e29e6e1e2810aafc5e7e20550eb6b7 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:35:53 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:25:25 (UTC) | 4 | 3.2 KB |