nf-core/bamutil/trimbam @ 0.0.0-0c7146d
Summary
trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
Get started
Add the following snippet to your workflow script to include this module.
include { BAMUTIL_TRIMBAM } from 'nf-core/bamutil/trimbam'
License
MIT License
Process
Name
|
BAMUTIL_TRIMBAM |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file *.bam
|
trim_left
integer
|
Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. |
trim_right
integer
|
Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. |
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Trimmed but unsorted BAM file *.bam
|
#2
versions_bamutil
tuple
${task.process}
string
|
The name of the process |
|---|---|
bamutil
string
|
The name of the tool |
bam trimBam 2>&1 | head -1 | sed 's/^Version: //;s/;.*//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bamutil | Programs that perform operations on SAM/BAM files, all built into a single executable, bam. | https://genome.sph.umich.edu/wiki/BamUtil |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:24:27 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbamutil%2Ftrimbam/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bamutil/trimbam/blobs/sha256:2ea0f5c9aba27074a9f60ecfe313f5c0a9d12e1e87c594aa92851ae548270af0 |
| Size | 2.4 KB |
| Checksum | sha256:2ea0f5c9aba27074a9f60ecfe313f5c0a9d12e1e87c594aa92851ae548270af0 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:24:27 (UTC) | 1 | 2.4 KB | - |