nf-core/samtools/import @ 0.0.0-0c7146d
Summary
converts FASTQ files to unmapped SAM/BAM/CRAM
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_IMPORT } from 'nf-core/samtools/import'
License
MIT License
Process
Name
|
SAMTOOLS_IMPORT |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
reads
file
|
fastq data to be converted to SAM/BAM/CRAM *.{fastq,fq,fastq.gz,fq.gz}
|
Output
4 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Unaligned BAM file *.bam
|
#2
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.sam
file
|
SAM file *.sam
|
#3
cram
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.cram
file
|
Unaligned CRAM file *.cram
|
#4
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 19:10:15 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fimport/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/import/blobs/sha256:8c403839f4aa576e40e56b0301dc2d68c7ead5edd1b56cd58bdc8558fc76f700 |
| Size | 2.9 KB |
| Checksum | sha256:8c403839f4aa576e40e56b0301dc2d68c7ead5edd1b56cd58bdc8558fc76f700 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:15 (UTC) | 1 | 2.9 KB | - |