nf-core/pairtools/parse @ 0.0.0-0c7146d
Summary
Find ligation junctions in .sam, make .pairs
Get started
Add the following snippet to your workflow script to include this module.
include { PAIRTOOLS_PARSE } from 'nf-core/pairtools/parse'
License
MIT License
Process
Name
|
PAIRTOOLS_PARSE |
|---|
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}
|
chromsizes
file
|
chromosome size file |
|---|
Output
3 channels
#1
stat
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.pairsam.stat
file
|
stats of the pairs *.{pairsam.stat}
|
#2
pairsam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.pairsam.gz
file
|
parsed pair file *.{pairsam.gz}
|
#3
versions_pairtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
pairtools
string
|
The name of the tool |
pairtools --version | sed 's/.*pairtools.*version //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| pairtools | CLI tools to process mapped Hi-C data | http://pairtools.readthedocs.io/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:22:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpairtools%2Fparse/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pairtools/parse/blobs/sha256:58864ee8e22829e3dd7905f198b05acfa7094ee32eb84593a7e4dacd5dd52bff |
| Size | 2.4 KB |
| Checksum | sha256:58864ee8e22829e3dd7905f198b05acfa7094ee32eb84593a7e4dacd5dd52bff |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:34:52 (UTC) | 3 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:25:00 (UTC) | 4 | 2.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:22:49 (UTC) | 4 | 2.4 KB |