nf-core/picard/cleansam @ 0.0.0-0c7146d
Summary
Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
Get started
Add the following snippet to your workflow script to include this module.
include { PICARD_CLEANSAM } from 'nf-core/picard/cleansam'
License
MIT License
Process
Name
|
PICARD_CLEANSAM |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file *.{bam}
|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Cleaned BAM file *.{bam}
|
#2
versions_picard
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
picard
string
|
The tool name |
picard CleanSam --version 2>&1 | sed -n 's/.*Version://p'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| picard | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | https://broadinstitute.github.io/picard/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:02:24 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcleansam/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/cleansam/blobs/sha256:e8d70101241f7af77e8af0b5a58c33fd8b5e8217e3adaf290b6fb1bbd925da64 |
| Size | 2.8 KB |
| Checksum | sha256:e8d70101241f7af77e8af0b5a58c33fd8b5e8217e3adaf290b6fb1bbd925da64 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:02:24 (UTC) | 1 | 2.8 KB | - |