nf-core/samtools/stats @ 0.0.0-0c7146d
Summary
Produces comprehensive statistics from SAM/BAM/CRAM file
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_STATS } from 'nf-core/samtools/stats'
License
MIT License
Process
Name
|
SAMTOOLS_STATS |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM file from alignment *.{bam,cram}
|
input_index
file
|
BAI/CRAI file from alignment *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
Reference file the CRAM was created with (optional) *.{fasta,fa,fna}
|
fai
file
|
FASTA ref index file *.{fasta,fa,fna}.fai
|
Output
2 channels
#1
stats
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.stats
file
|
File containing samtools stats output *.{stats}
|
#2
versions_samtools
tuple
${task.process}
string
|
Name of the process |
|---|---|
samtools
string
|
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 19:10:36 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fstats/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/stats/blobs/sha256:6b397075c9ca3834603001ba3f18e678a4039aba116ec09193c1b75aaf90ff08 |
| Size | 2.8 KB |
| Checksum | sha256:6b397075c9ca3834603001ba3f18e678a4039aba116ec09193c1b75aaf90ff08 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:36 (UTC) | 1 | 2.8 KB | - |