Description

Map reads from a FASTx file to a reference in chunks, outputting the alignments in BAM or PAF format. If BAM alignment is chosen, the output BAM files are merged.

Input

Name
Description
Pattern

ch_assemblies

Assemblies to map reads to, in FASTA format. Can be gzipped. Structure: [ val(meta), path(fasta) ]

ch_fasta

Reads to map to assemblies, in FASTA or FASTQ format. Can be gzipped. Structure: [ val(meta), path(fasta) ] or [ val(meta), [ path(fasta1), path(fasta2) ... ] ]

val_reads_per_fasta_chunk

Number of reads to map per chunk of FASTA file. A sensible value for long reads might be 1,000,000.

val_output_bam

Boolean. If true, output alignments in BAM format. Otherwise, alignments are output in unmerged unsorted PAF format.

Output

Name
Description
Pattern

bam (file)

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

*.bam

bam_index (file)

Channel containing index files for output BAM Structure: [ val(meta), path(index) ]

*.{bai,csi,crai}

paf (file)

Channel containing PAF files Structure: [ val(meta), path(paf) ]

*.paf

Components

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