modules/biscuit_biscuitblaster

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

biscuitDNA methylationWGBSscWGBSbisulfite sequencingalignerbam

https://github.com/nf-core/modules/[...]/modules/nf-core/biscuit/biscuitblaster

Description

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

Input

name:type

description

pattern

`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.

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

Input genome fasta file

`meta3`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`index`
`:directory`

Directory containing biscuit genome index

Output

name:type

description

pattern

`bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.bam`
`:file`

Output BAM file containing read alignments

*.{bam}

`bai`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.bai`
`:file`

Output BAM index

*.{bai}

`versions_biscuit`

`${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

`versions_samtools`

`${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

`versions_samblaster`

`${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

Topics

name:type

description

pattern

`versions`

`${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

`${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

`${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

Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/biscuitblaster https://github.com/huishenlab/biscuit

samblaster
MIT

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.

github.com/GregoryFaust/samblaster 10.1093/bioinformatics/btu314

samtools
MIT

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 http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

modules/biscuit_biscuitblaster

Description

Input

meta:map

reads:file

meta2:map

fasta:file

meta3:map

index:directory

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

versions_biscuit

${task.process}:string

biscuit:string

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //':eval

versions_samtools

${task.process}:string

samtools:string

samtools --version |& sed '1!d; s/^.*samtools //':eval

versions_samblaster

${task.process}:string

samblaster:string

samblaster --version |& sed 's/^.*samblaster: Version //':eval

Topics

versions

${task.process}:string

biscuit:string

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //':eval

${task.process}:string

samtools:string

samtools --version |& sed '1!d; s/^.*samtools //':eval

${task.process}:string

samblaster:string

samblaster --version |& sed 's/^.*samblaster: Version //':eval

Tools

biscuit MIT

samblaster MIT

samtools MIT

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`index`
`:directory`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`versions_biscuit`

`${task.process}`
`:string`

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

`versions_samblaster`

`${task.process}`
`:string`

`samblaster`
`:string`

`samblaster --version |& sed 's/^.*samblaster: Version //'`
`:eval`

`versions`

`${task.process}`
`:string`

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

`${task.process}`
`:string`

`samblaster`
`:string`

`samblaster --version |& sed 's/^.*samblaster: Version //'`
`:eval`

biscuit
MIT

samblaster
MIT

samtools
MIT