Description

Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.

Input

name:type
description
pattern

meta:map

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

]

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

]

fasta:file

Input genome fasta file

meta3:map

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

]

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

]

*.bam:file

Output BAM file containing read alignments

*.{bam}

bai

meta:map

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

]

*.bai:file

Output BAM index

*.{bai}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

biscuit
MIT

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

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/docs/alignment https://github.com/huishenlab/biscuit
maintainers
Github user njspix
Github user sateeshperi
get in touch
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