Description

Map read inputs and emit alignment and coverage bedGraph outputs

Input

Name
Description
Pattern

ch_reference (file)

Channel containing reference assembly FASTA files used for mapping. Structure: [ val(meta), path(reference_fasta) ]

*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}

ch_reads (file)

Channel containing read data, restricted to gzipped FASTA/FASTQ. Structure: [ val(meta), path(reads) ] or [ val(meta), [ path(reads1), path(reads2), ... ] ]

*.{fasta.gz,fastq.gz,fa.gz,fq.gz}

Output

Name
Description
Pattern

bigwig (file)

Coverage BigWig generated from bedGraph. Structure: [ val(meta), path(bigwig) ]

*.bw

bedgraph (file)

Coverage bedGraph output generated from MINIMAP2_ALIGN outputs. Structure: [ val(meta), path(bedgraph) ]

*.bedgraph

Components

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