Description

Purge retained haplotypic duplications from an assembly using purge_dups.

If alternate assembly or alternate assemblies are provided, these will all be concatenated with the purged haplotigs.

Input

Name
Description
Pattern

ch_assemblies (file)

Input assemblies for purging in FASTA format. Should be a list with the primary haplotype in the first position. The list can be of length 1 if there are no alternates. Must be uncompressed.

Structure: [val(meta), [path(fasta1), path(fasta2), ...]]

*.{fasta,fa}

ch_long_reads (file)

Reads to map to the primary assembly to determine base-level coverage.

Structure: [ val(meta), [path(fasta)... ] ]

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

val_fastx_reads_per_chunk (integer)

How many reads to map to the primary in a single chunk.

Output

Name
Description
Pattern

purged_assemblies (file)

Channel containing the purged primary assembly, and alternate assembly with purged haplotigs appended.

Structure: [ val(meta), path(fasta), path(fasta) ]

*.fa

purged_haplotigs (file)

Channel containing just the haplotig sequence that was purged from the primary assembly.

Structure: [ val(meta), path(fasta) ]

*.fa

purgedups_pbcstat_hist (file)

Channel containing the read depth histogram

Structure: [ val(meta), path(csi) ]

*.stat

purgedups_pbcstat_basecov (file)

Channel containing base-level read depth of the contigs

Structure: [ val(meta), path(bae) ]

*.base.cov

purgedups_calcuts_cutoffs (file)

Channel containing the purge_dups cutoffs file

Structure: [ val(meta), path(cutoffs) ]

*.cutoffs

purgedups_calcuts_log (file)

Channel containing the log file from cutoff calculation

Structure: [ val(meta), path(log) ]

*.cutoffs.log

purgedups_bed (file)

Channel containing the BED file describing regions to purge

Structure: [ val(meta), path(bed) ]

*.bed.gz

purgedups_log (file)

Channel containing the log file from purge_dups

Structure: [ val(meta), path(log) ]

*.log

Components

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