nf-core/samtools/samples @ 0.0.0-0c7146d
Summary
Write sample names and path to reference genome of an alignment to a text file.
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_SAMPLES } from 'nf-core/samtools/samples'
License
MIT License
Process
Name
|
SAMTOOLS_SAMPLES |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information. e.g. |
|---|---|
bam
file
|
alignment file *.{bam,sam,cram}
|
bai
file
|
index file for the alignment *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information. |
|---|---|
fasta
file
|
reference genome file (optional) *.{fasta,fa,fna}
|
fai
file
|
index file for the reference genome (optional) *.fai
|
Output
2 channels
#1
tsv
tuple
meta
map
|
Groovy Map containing sample information. e.g. |
|---|---|
*.tsv
file
|
tab-separated file containing sample names, BAM filename and optionally reference genome path *.tsv
|
#2
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed '1!d;s/.* //'
string
|
The command used to generate 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 19:10:29 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fsamples/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/samples/blobs/sha256:d66bc28019a368924aef454f3aed89ff699b63667e9527a56c055910790490c0 |
| Size | 3.1 KB |
| Checksum | sha256:d66bc28019a368924aef454f3aed89ff699b63667e9527a56c055910790490c0 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:29 (UTC) | 1 | 3.1 KB | - |