Nextflow Registry | nf-core/pbtk/bam2fastq@0.0.0-0c7146d

nf-core/pbtk/bam2fastq @ 0.0.0-0c7146d

converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq

convert bam genomics pacbio

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @mbeavitt @gallvp

Maintainers: @mbeavitt @gallvp

converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq

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

include { PBTK_BAM2FASTQ } from 'nf-core/pbtk/bam2fastq'

MIT License

Process

`Name`	`PBTK_BAM2FASTQ`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`bam` file	PacBio BAM file `*.bam`
`pbi` file	PacBio BAM file index (.pbi) `*.pbi`

Output 2 channels

#1 fastq tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.$extension` file	Gzipped FASTQ file `*.fastq.gz`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
pbtk	pbtk - PacBio BAM toolkit	https://github.com/PacificBiosciences/pbtk

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:01:48 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpbtk%2Fbam2fastq/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pbtk/bam2fastq/blobs/sha256:1246007871513745a453ded92cf8131f61b8925b243c244008f608abced48fc1
Size	2.4 KB
Checksum	sha256:1246007871513745a453ded92cf8131f61b8925b243c244008f608abced48fc1
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:01:48 (UTC)		1	2.4 KB	-