Nextflow Registry | nf-core/pbtk/bam2fastq@0.0.0-3fc6d40

nf-core/pbtk/bam2fastq @ 0.0.0-3fc6d40

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

convert bam genomics pacbio

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:25:28 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpbtk%2Fbam2fastq/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pbtk/bam2fastq/blobs/sha256:c613442a60500e75e3b9e2fe5e180814017ef1596c5c165a39c96406ede63649
Size	2.5 KB
Checksum	sha256:c613442a60500e75e3b9e2fe5e180814017ef1596c5c165a39c96406ede63649
Downloads	1

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:35:26 (UTC)	3	2.4 KB
0.0.0-3fc6d40	22 Apr 2026 15:25:28 (UTC)	1	2.5 KB
0.0.0-0c7146d	08 Apr 2026 19:24:46 (UTC)	3	2.4 KB