Nextflow Registry | nf-core/samtools/import@0.0.0-6c4ed3a

nf-core/samtools/import @ 0.0.0-6c4ed3a

converts FASTQ files to unmapped SAM/BAM/CRAM

import fastq bam sam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @matthdsm

Maintainers: @matthdsm

converts FASTQ files to unmapped SAM/BAM/CRAM

Add the following snippet to your workflow script to include this module.

include { SAMTOOLS_IMPORT } from 'nf-core/samtools/import'

MIT License

Process

`Name`	`SAMTOOLS_IMPORT`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`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. `[ id:'test', single_end:false ]`
`*.bam` file	Unaligned BAM file `*.bam`

#2 sam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.sam` file	SAM file `*.sam`

#3 cram tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:42:27 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fimport/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/import/blobs/sha256:bd14e29213d37a4b5f61727bff55bc0c9fa04ffdf8e5878ace5dfd76d77c344a
Size	2.9 KB
Checksum	sha256:bd14e29213d37a4b5f61727bff55bc0c9fa04ffdf8e5878ace5dfd76d77c344a
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:42:27 (UTC)		3	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:33:54 (UTC)		3	2.9 KB