bam_taps_conversion

Uses rastair to assess C->T conversion as a readout for methylation in a genome-wide basis

TAPS conversionMethylation analysisMolecular bias (MBIAS)mCtoTrastair4-letter genome

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_taps_conversion

Description

Uses rastair to assess C->T conversion as a readout for methylation in a genome-wide basis

Input

name

description

pattern

`ch_fasta`

Reference genome fasta file
Structure: [ [:], path(fasta) ]

*.{fa,fasta}

`ch_fasta_index`

Reference genome index file
Structure: [ val(meta), path(fai) ]

*.fai

`ch_bam`

BAM alignment files
Structure: [ val(meta), path(bam) ]

*.bam

`ch_bai`

BAM index files
Structure: [ val(meta), path(bai) ]

*.bai

Output

name

description

pattern

`mbias`

File describing the molecular bias (MBIAS) of the TAPS conversion
Structure: [ val(meta), path(mbias) ]

*.txt

`call`

Rastair call output files (similar to bed format, genome-wide)
Structure: [ val(meta), path(call) ]

*.txt

`methylkit`

Rastair call output files in MethylKit format (similar to bed format, genome-wide)
Structure: [ val(meta), path(methylkit) ]

*.gz