nf-core/bamutil/trimbam @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:04:29 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbamutil%2Ftrimbam/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bamutil/trimbam/blobs/sha256:6a0d00c52a753dde88ee427540ae3b0c495e1806cdb77a2bb10bf1dad92e6e7e |
| Size | 2.4 KB |
| Checksum | sha256:6a0d00c52a753dde88ee427540ae3b0c495e1806cdb77a2bb10bf1dad92e6e7e |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:04:29 (UTC) | 3 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:21 (UTC) | 1 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:45:10 (UTC) | 4 | 2.4 KB |