Nextflow Registry | nf-core/biscuit/biscuitblaster@0.0.0-6c4ed3a

nf-core/biscuit/biscuitblaster @ 0.0.0-6c4ed3a

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @njspix

Maintainers: @njspix @sateeshperi

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

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

include { BISCUIT_BLASTER } from 'nf-core/biscuit/biscuitblaster'

MIT License

Process

`Name`	`BISCUIT_BLASTER`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Input genome fasta file

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`index` directory	Directory containing biscuit genome index

Output 5 channels

#1 bai tuple

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

#2 bam tuple

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

#3 versions_biscuit tuple

`${task.process}` string	The name of the process
`biscuit` string	The name of the tool
`biscuit version \|& sed '1!d; s/^.*BISCUIT Version: //'` eval	The expression to obtain the version of the tool

#4 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools --version \|& sed '1!d; s/^.*samtools //'` eval	The expression to obtain the version of the tool

#5 versions_samblaster tuple

`${task.process}` string	The name of the process
`samblaster` string	The name of the tool
`samblaster --version \|& sed 's/^.*samblaster: Version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
biscuit	A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data	https://huishenlab.github.io/biscuit/
samblaster	samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout.	n/a
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 15:06:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiscuit%2Fbiscuitblaster/0.0.0-6c4ed3a/download