nf-core/samtools/flagstat @ 0.0.0-0c7146d
Summary
Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_FLAGSTAT } from 'nf-core/samtools/flagstat'
License
MIT License
Process
Name
|
SAMTOOLS_FLAGSTAT |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
bai
file
|
Index for BAM/CRAM/SAM file *.{bai,crai,sai}
|
Output
2 channels
#1
flagstat
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.flagstat
file
|
File containing samtools flagstat output *.{flagstat}
|
#2
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 |
| Tool | Description | Homepage |
|---|---|---|
| samtools | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. | http://www.htslib.org/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:10:10 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fflagstat/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/flagstat/blobs/sha256:5d9a0500e915a464b9a66f3fc23f8ecbe9a6525112b49e204abfc75ccdeb54e8 |
| Size | 2.6 KB |
| Checksum | sha256:5d9a0500e915a464b9a66f3fc23f8ecbe9a6525112b49e204abfc75ccdeb54e8 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:10 (UTC) | 1 | 2.6 KB | - |