nf-core/bamclipper @ 0.0.0-02a6b4c
Summary
This module is used to clip primer sequences from your alignments.
Get started
Add the following snippet to your workflow script to include this module.
include { BAMCLIPPER } from 'nf-core/bamclipper'
License
MIT License
Process
Name
|
BAMCLIPPER |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
bam
file
|
Sorted BAM file *.bam
|
bai
file
|
BAI index of the input BAM file *.bam.bai
|
bedpe
file
|
BEDPE file of primer pair locations *.bed
|
Output
4 channels
#1
bai
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.primerclipped.bam.bai
file
|
BAI index of the output BAM file *.primerclipped.bam.bai
|
#2
bam
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.primerclipped.bam
file
|
Sorted BAM file containing clipped query sequences according to the given primer pair locations *.primerclipped.bam
|
#3
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 |
#4
versions_bamclipper
tuple
${task.process}
string
|
The name of the process |
|---|---|
bamclipper
string
|
The name of the tool |
1.0.0
string
|
The hardcoded version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bamclipper | BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing | https://github.com/tommyau/bamclipper |
| Version | 0.0.0-02a6b4c |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 13 Apr 2026 15:00:08 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbamclipper/0.0.0-02a6b4c/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bamclipper/blobs/sha256:b5a04a1d1459393a4a78e5dc6290e8e0ce74b1b52de652f8575a62a71df2dfcd |
| Size | 2.5 KB |
| Checksum | sha256:b5a04a1d1459393a4a78e5dc6290e8e0ce74b1b52de652f8575a62a71df2dfcd |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:03:19 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:36 (UTC) | 3 | 2.5 KB | |
| 0.0.0-7f68141 | 16 Apr 2026 15:00:07 (UTC) | 4 | 2.5 KB | |
| 0.0.0-02a6b4c | 13 Apr 2026 15:00:08 (UTC) | 3 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:44:10 (UTC) | 3 | 2.5 KB |