nf-core/picard/filtersamreads @ 0.0.0-6c4ed3a
Summary
Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
Get started
Add the following snippet to your workflow script to include this module.
include { PICARD_FILTERSAMREADS } from 'nf-core/picard/filtersamreads'
License
MIT License
Process
Name
|
PICARD_FILTERSAMREADS |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam *.{bam}
|
readlist
file
|
Optional text file containing reads IDs to include or exclude |
filter
string
|
Picard filter type includeAligned|excludeAligned|includeReadList|excludeReadList
|
|---|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Filtered BAM file *.{bam}
|
#2
versions_picard
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
picard
string
|
The tool name |
picard FilterSamReads --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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:36:07 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Ffiltersamreads/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/filtersamreads/blobs/sha256:79a7d93f02db264e2beca3d16a7d3223fb3a71fada0d22e10fbc086ccca87ff5 |
| Size | 3.2 KB |
| Checksum | sha256:79a7d93f02db264e2beca3d16a7d3223fb3a71fada0d22e10fbc086ccca87ff5 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:36:07 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:25:46 (UTC) | 2 | 3.2 KB |