Nextflow Registry | nf-core/gatk4/printreads@0.0.0-0c7146d

nf-core/gatk4/printreads @ 0.0.0-0c7146d

Print reads in the SAM/BAM/CRAM file

bam cram gatk4 printreads sam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Print reads in the SAM/BAM/CRAM file

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

include { GATK4_PRINTREADS } from 'nf-core/gatk4/printreads'

MIT License

Process

`Name`	`GATK4_PRINTREADS`

Input 4 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	reference fasta file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	reference fasta index file `*.{fai}`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`dict` file	reference fasta dictionary file `*.{dict}`

Output 4 channels

#1 bam tuple

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

#2 sam tuple

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

#3 cram tuple

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

#4 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk4	Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:42:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fprintreads/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/printreads/blobs/sha256:b89b599280ac4419f9267086341762f33b2b6260d2034eb0d3ed51c6faca5734
Size	3.0 KB
Checksum	sha256:b89b599280ac4419f9267086341762f33b2b6260d2034eb0d3ed51c6faca5734
Downloads	1