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

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

convert and then index CRAM -> BAM or BAM -> CRAM file

view index bam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @FriederikeHanssen @maxulysse

Maintainers: @FriederikeHanssen @maxulysse @matthdsm

convert and then index CRAM -> BAM or BAM -> CRAM file

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

include { SAMTOOLS_CONVERT } from 'nf-core/samtools/convert'

MIT License

Process

`Name`	`SAMTOOLS_CONVERT`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file `*.{bam,cram}`
`index` file	BAM/CRAM index file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Reference file to create the CRAM file `*.{fasta,fa}`
`fai` file	Reference index file to create the CRAM file `*.{fai}`

Output 5 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bai` file	filtered/converted BAM index `*{.bai}`

#2 bam tuple

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

#3 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.crai` file	filtered/converted CRAM index `*{.crai}`

#4 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	filtered/converted CRAM file `*{cram}`

#5 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The 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 15:42:13 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fconvert/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/convert/blobs/sha256:e04e979c604330fb1f5abce00163485b84b2194ac14b2f01a1f69bf0f3868a4c
Size	2.9 KB
Checksum	sha256:e04e979c604330fb1f5abce00163485b84b2194ac14b2f01a1f69bf0f3868a4c
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a