nf-core/samclip @ 0.0.0-0c7146d
Summary
Filters SAM/BAM/CRAM files for soft and hard clipped alignments
Get started
Add the following snippet to your workflow script to include this module.
include { SAMCLIP } from 'nf-core/samclip'
License
MIT License
Process
Name
|
SAMCLIP |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
BAM file *.bam
|
#2
tuple
meta2
map
|
Groovy Map containing fasta reference information e.g. |
|---|---|
reference
file
|
reference FASTA file *.{fasta,fa,fasta.gz,fa.gz}
|
reference_index
file
|
reference FASTA file index *.fai
|
Output
3 channels
#1
reads
tuple
meta
map
|
Groovy Map containing sample information. e.g. |
|---|---|
*.{bam,cram}
file
|
Filtered BAM/CRAM file *.{bam,cram}
|
#2
versions_samclip
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samclip
string
|
The tool name |
samclip --version | sed 's/^.*samclip //g'
string
|
The command used to generate the version of the tool |
#3
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed '1!d;s/.* //'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samclip | Filters SAM file for soft and hard clipped alignments | https://github.com/tseemann/samclip |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:09:31 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamclip/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samclip/blobs/sha256:532c8948a2e18f4a1d41d8e4f20692d16cfb91f73c83c52fa69171ede411b8f6 |
| Size | 2.9 KB |
| Checksum | sha256:532c8948a2e18f4a1d41d8e4f20692d16cfb91f73c83c52fa69171ede411b8f6 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:09:31 (UTC) | 1 | 2.9 KB | - |