Description

Maps PacBio/ONT reads in unaligned CRAMs format to a set of references.

Input

Name
Description
Pattern

ch_assemblies (file)

Input channel containing assemblies to align PacBio/ONT reads to Structure: [ val(meta), path(fasta) ]

*.fn?a(sta)?(.gz)?

ch_crams (file)

Input channel containing PacBio/ONT CRAM files for mapping. Structure: [ val(meta), path(cram) ] or [ val(meta), [ path(cram1), path(cram2), ... ] ]

*.cram

val_cram_chunk_size (integer)

Size of chunk to split CRAM files into

Output

Name
Description
Pattern

bam (file)

Channel containing the BAM files describing long-read alignments to the input assemblies Structure: [ val(meta), path(bam) ]

*.bam

Components

Command copied!