fastq_align_dedup_bwameth
Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate
bwamethalignment3-letter genomemapmethylation5mCmethylseqbisulphitebisulfitefastqbam
Description
Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate
Input
name
description
pattern
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}
Output
name
description
pattern
File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]
*.flagstat
File containing samtools stats output
Structure: [ val(meta), path(stats) ]
*.{stats}
Duplicate metrics file generated by picard
Structure: [ val(meta), path(metrics) ]
*.{metrics.txt}
Channel containing MultiQC report aggregating results across samples.
Structure: [ val(meta), path(multiqc_report.html) ]
*.html