nf-core/samtools/collate @ 0.0.0-0c7146d
Summary
shuffles and groups reads together by their names
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_COLLATE } from 'nf-core/samtools/collate'
License
MIT License
Process
Name
|
SAMTOOLS_COLLATE |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
Reference genome file *.{fa,fasta}
|
fai
file
|
Reference genome index file *.fai
|
Output
4 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Sorted BAM *.{bam}
|
#2
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.sam
file
|
Sorted SAM *.{sam}
|
#3
cram
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.cram
file
|
Sorted CRAM *.{cram}
|
#4
versions_samtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
samtools
string
|
The name of the tool |
samtools version | sed '1!d;s/.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files | http://www.htslib.org |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:33:26 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fcollate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/collate/blobs/sha256:8870f8e03afcf96b3054bf7829b18e861146df327925aa1ee277f2bb197dc20d |
| Size | 2.7 KB |
| Checksum | sha256:8870f8e03afcf96b3054bf7829b18e861146df327925aa1ee277f2bb197dc20d |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:42:09 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:26 (UTC) | 3 | 2.7 KB |