fastq_align_dedup_bismark

Align BS-Seq reads to a reference genome using bismark, deduplicate and sort

bismark3-letter genomemapmethylation5mCmethylseqbisulphitebisulfitebam

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

Description

Align BS-Seq reads to a reference genome using bismark, deduplicate and sort

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_bismark_index`

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

BismarkIndex

`skip_deduplication`

Skip deduplication of aligned reads

`cytosine_report`

Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts

Output

name

description

pattern

`bam`

Channel containing aligned or deduplicated BAM files.
Structure: [ val(meta), path(bam) ]

*.bam

`bai`

Channel containing aligned or deduplicated BAM index files.
Structure: [ val(meta), path(bam.bai) ]

*.bai

`coverage2cytosine_coverage`

Channel containing coverage information from coverage2cytosine.
Structure: [ val(meta), path(coverage.txt) ]

*.cov.gz

`coverage2cytosine_report`

Channel containing report from coverage2cytosine summarizing cytosine methylation coverage.
Structure: [ val(meta), path(report.txt) ]

*report.txt.gz

`coverage2cytosine_summary`

Channel containing summary information from coverage2cytosine.
Structure: [ val(meta), path(summary.txt) ]

*cytosine_context_summary.txt

`methylation_bedgraph`

Channel containing methylation data in bedGraph format.
Structure: [ val(meta), path(methylation.bedgraph) ]

*.bedGraph.gz

`methylation_calls`

Channel containing methylation call data.
Structure: [ val(meta), path(calls.txt) ]

*.txt.gz

`methylation_coverage`

Channel containing methylation coverage data.
Structure: [ val(meta), path(coverage.txt) ]

*.cov.gz

`methylation_report`

Channel containing methylation report detailing methylation patterns.
Structure: [ val(meta), path(report.txt) ]

*_splitting_report.txt

`methylation_mbias`

Channel containing M-bias report showing methylation bias across read positions.
Structure: [ val(meta), path(mbias.txt) ]

*.M-bias.txt

`bismark_report`

Channel containing Bismark report with mapping and methylation statistics.
Structure: [ val(meta), path(bismark_report.txt) ]

*report.{html,txt}

`bismark_summary`

Channel containing Bismark summary report.
Structure: [ val(meta), path(bismark_summary.txt) ]