fastq_align_dedup_bwameth

Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate

bwamethalignment3-letter genomemapmethylation5mCmethylseqbisulphitebisulfitefastqbam

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

Description

Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate

Input

name

description

pattern

`ch_reads`

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]

*.{fastq,fastq.gz}

`ch_fasta`

Structure: [ val(meta), path(fasta) ]

*.{fa,fa.gz}

`ch_fasta_index`

Structure: [ val(meta), path(fasta index) ]

`ch_bwameth_index`

Bismark genome index files
Structure: [ val(meta), path(index) ]

BismarkIndex

`skip_deduplication`

Skip deduplication of aligned reads

`use_gpu`

Use GPU for alignment

Output

name

description

pattern

`bam`

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

*.bam

`bai`

Channel containing indexed BAM (BAI) files
Structure: [ val(meta), path(bai) ]

*.bai

`samtools_flagstat`

File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]

*.flagstat

`samtools_stats`

File containing samtools stats output
Structure: [ val(meta), path(stats) ]

*.{stats}

`methydackel_extract_bedgraph`

bedGraph file, containing per-base methylation metrics
Structure: [ val(meta), path(bedgraph) ]

*.bedGraph

`methydackel_extract_methylkit`

methylKit file, containing per-base methylation metrics
Structure: [ val(meta), path(methylKit) ]

*.methylKit

`methydackel_mbias`

Text file containing methylation bias
Structure: [ val(meta), path(mbias) ]

*.{txt}

`picard_metrics`

Duplicate metrics file generated by picard
Structure: [ val(meta), path(metrics) ]

*.{metrics.txt}

`multiqc`

Channel containing MultiQC report aggregating results across samples.
Structure: [ val(meta), path(multiqc_report.html) ]

*.html

`versions`

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml