Description

Generate the accessory files needed for pretext ingestion

Input

Name
Description
Pattern

ch_reference_tuple (file)

Input fasta reference assembly.

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

*.{fasta,fa,fna}

ch_reference_sizes (file)

Input chromosome sizes file - a TSV with two columns (name and size) and no header line.

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

*.{sizes,tsv}

ch_longread_reads (file)

Input array of read files used for coverage mapping.

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

[*.{fasta.gz}]

val_teloseq (string)

A telomeric motif sequence

val_split_telomere (boolean)

Whether to split the telomere file into forward, reverse and whole files.

val_run_telomere (boolean)

Run the telomere file generation subworkflow

val_run_gaps (boolean)

Run the gap file generation subworkflow

val_run_coverage (boolean)

Run coverage file generation subworkflow

val_run_repeat_den (boolean)

Run the repeat density file generation subworkflow

val_run_busco_track (boolean)

Run the busco file generation subworkflow

val_run_pebble (boolean)

Run pebble coverage file generation subworkflow

Output

Name
Description
Pattern

gap_file (file)

Gap file in bed 4 format. Structure: [ val(meta), path(bed) ]

*.bed

gap_bed_and_index (file)

Gap file in bed 4 format. Structure: [ val(meta), path(bed), path(csi) ]

*.gz | *.csi

repeat_file (file)

Repeat density file in bigwig format. Structure: [ val(meta), path(bigwig) ]

*.bigwig

telo_file (file)

Telomere file array, which can consist of an array of 3 bed files Structure: [ val(meta), path(bed) ]

*.bed

telo_windows (file)

Telomere window file array, which can consist of an array of 3 files Structure: [ val(meta), path(windows) ]

*.bed

telo_bed_and_index (file)

Telomere file in bed 4 format. Structure: [ val(meta), path(bed), path(csi) ]

*.gz | *.csi

coverage_file (file)

Coverage file in bigwig format. Structure: [ val(meta), path(bigwig) ]

*.bigwig

Components

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