nf-core/samtools/stats @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:43:28 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fstats/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/stats/blobs/sha256:ad46da738c731635fbf7b64ca2dc2cecac78dfec180034334addfa99929c02df |
| Size | 2.8 KB |
| Checksum | sha256:ad46da738c731635fbf7b64ca2dc2cecac78dfec180034334addfa99929c02df |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:43:28 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:34:15 (UTC) | 4 | 2.8 KB |