nf-core/samclip @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:41:58 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamclip/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samclip/blobs/sha256:63bbddc8998f8b4aef0d117ea44288f5737ef92c181f6fc6621e385f72fa1a5c |
| Size | 2.9 KB |
| Checksum | sha256:63bbddc8998f8b4aef0d117ea44288f5737ef92c181f6fc6621e385f72fa1a5c |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:41:58 (UTC) | 4 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:10 (UTC) | 4 | 2.9 KB |