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DLBPointonDLBPointon
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Update Minor things
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  • modules/local/pretext/graph
  • subworkflows/local/telo_finder

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‎modules/local/pretext/graph/main.nf‎

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process PRETEXT_GRAPH {
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tag "$meta.id"
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label 'process_single'
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container "quay.io/sanger-tol/pretext:0.0.9-yy5-c2"
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input:
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tuple val(meta), path(pretext_file)
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path(gap_file, stageAs: 'gap_file.bed')
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path(coverage, stageAs: 'coverage.bw')
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path(telomere_file, stageAs: 'telomere/*')
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path(repeat_density, stageAs: 'repeat_density.bw')
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val (split_telo_bool)
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output:
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tuple val(meta), path("*.pretext") , emit: pretext
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PRETEXT GRAPH module does not _currently_ support Conda. Please use Docker / Singularity instead."
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}
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def UCSC_VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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// Using single [ ] as nextflow will use sh where possible not bash
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// Duplicate the telo chunk for the 5' and 3' and then another telox
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"""
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shopt -s nullglob
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echo "PROCESSING ESSENTIAL FILES"
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if [ -s "${coverage}" ]; then
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echo "PROCESSING COVERAGE..."
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bigWigToBedGraph ${coverage} /dev/stdout | PretextGraph ${args} -i ${pretext_file} -n "coverage" -o coverage.pretext.part
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else
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echo "SKIPPING COVERAGE"
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mv ${pretext_file} coverage.pretext.part
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fi
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if [ -s "${repeat_density}" ]; then
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echo "PROCESSING REPEAT_DENSITY..."
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bigWigToBedGraph ${repeat_density} /dev/stdout | PretextGraph ${args} -i coverage.pretext.part -n "repeat_density" -o repeat.pretext.part
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else
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echo "SKIPPING REPEAT_DENSITY"
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mv coverage.pretext.part repeat.pretext.part
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fi
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echo "NOW PROCESSING NON-ESSENTIAL files"
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input_file="repeat.pretext.part"
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if [ -s "${gap_file}" ]; then
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echo "Processing GAP file..."
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cat "${gap_file}" | PretextGraph ${args} -i repeat.pretext.part -n "gap" -o gap.pretext.part
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input_file="gap.pretext.part"
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fi
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mkdir -p telomere/
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if [ -n "\$(ls -A telomere/ 2>/dev/null)" ]; then
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FILES=(telomere/*.bedgraph);
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echo "Found /telomere/ has contents:"
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file_telox=""
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file_5p=""
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file_3p=""
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file_og=""
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for file in telomere/*.bedgraph; do
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[ -e "\$file" ] || continue # skip if no match
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fname=\$(basename "\$file")
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case "\$fname" in
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*telox*)
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echo "Found TELOX: \$file"
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file_telox="\$file"
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;;
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*5P*)
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echo "Found 5P: \$file"
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file_5p="\$file"
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;;
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*3P*)
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echo "Found 3P: \$file"
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file_3p="\$file"
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;;
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*)
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echo "Found OG: \$file"
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file_og="\$file"
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;;
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esac
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done
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if [ -s "\$file_og" ]; then
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echo "Processing OG_TELOMERE file..."
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cat "\$file_og" | PretextGraph ${args} -i "\$input_file" -n "og_telomere" -o telo_0.pretext
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else
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mv "\$input_file" telo_0.pretext
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fi
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if [ -s "\$file_telox" ]; then
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echo "Processing TELOX_TELOMERE file..."
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cat "\$file_telox}" | PretextGraph ${args} -i telo_0.pretext -n "telox_telomere" -o telo_1.pretext
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else
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mv telo_0.pretext telo_1.pretext
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fi
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if [ -s "\$file_5p" ]; then
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echo "Processing 5 Prime TELOMERE file..."
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cat "\$file_5p" | PretextGraph ${args} -i telo_1.pretext -n "5p_telomere" -o telo_2.pretext
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else
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mv telo_1.pretext telo_2.pretext
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fi
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if [ -s "\$file_3p" ]; then
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echo "Processing 3 Prime TELOMERE file..."
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cat "\$file_3p" | PretextGraph ${args} -i telo_2.pretext -n "3p_telomere" -o "${prefix}.pretext"
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else
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mv telo_2.pretext "${prefix}.pretext"
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fi
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else
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mv "\$input_file" "${prefix}.pretext"
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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PretextGraph: \$(PretextGraph | grep "Version" | sed 's/Pretext.* Version //;')
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PretextMap: \$(PretextMap | grep "Version" | sed 's/Pretext.* Version//;')
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bigWigToBedGraph: ${UCSC_VERSION}
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END_VERSIONS
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"""
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stub:
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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error "PRETEXT GRAPH module does not _currently_ support Conda. Please use Docker / Singularity instead."
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}
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def prefix = task.ext.prefix ?: "${meta.id}"
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def UCSC_VERSION = '448' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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touch ${prefix}.pretext
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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PretextGraph: \$(PretextGraph | grep "Version" | sed 's/Pretext* Version //;')
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PretextMap: \$(PretextMap | grep "Version" | sed 's/PretextMap Version//;')
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bigWigToBedGraph: ${UCSC_VERSION}
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END_VERSIONS
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"""
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}

‎subworkflows/local/telo_finder/main.nf‎

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#!/usr/bin/env nextflow
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//
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// MODULE IMPORT BLOCK
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//
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include { GAWK as GAWK_UPPER_SEQUENCE } from '../../../modules/nf-core/gawk/main'
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include { FIND_TELOMERE_REGIONS } from '../../../modules/local/find/telomere_regions/main'
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include { GAWK as GAWK_SPLIT_DIRECTIONS } from '../../../modules/local/gawk/main'
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include { TELO_EXTRACTION } from '../../../subworkflows/local/telo_extraction/main'
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workflow TELO_FINDER {
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take:
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reference_tuple // Channel: tuple [ val(meta), path(fasta) ]
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teloseq
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main:
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ch_versions = Channel.empty()
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//
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// MODULE: UPPERCASE THE REFERENCE SEQUENCE
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//
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GAWK_UPPER_SEQUENCE(
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reference_tuple,
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[],
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false,
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)
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ch_versions = ch_versions.mix( GAWK_UPPER_SEQUENCE.out.versions )
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//
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// MODULE: FINDS THE TELOMERIC SEQEUNCE IN REFERENCE
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//
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FIND_TELOMERE_REGIONS (
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GAWK_UPPER_SEQUENCE.out.output,
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teloseq
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)
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ch_versions = ch_versions.mix( FIND_TELOMERE_REGIONS.out.versions )
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//
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// MODULE: SPLIT THE TELOMERE FILE INTO 5' and 3' FILES
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// THIS IS RUNNING ON A LOCAL VERSION OF THE GAWK MODULE
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//
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if (params.split_telomere) {
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GAWK_SPLIT_DIRECTIONS (
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FIND_TELOMERE_REGIONS.out.telomere,
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file("${projectDir}/bin/gawk_split_directions.awk"),
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false
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)
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ch_versions = ch_versions.mix( GAWK_SPLIT_DIRECTIONS.out.versions )
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GAWK_SPLIT_DIRECTIONS.out.prime5
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.map { meta, file ->
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tuple( [id: meta.id + "5P" + prime], file)
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}
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.set { prime5_telo }
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GAWK_SPLIT_DIRECTIONS.out.prime3
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.map { meta, file ->
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tuple( [id: meta.id + "3P" + prime], file)
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}
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.set { prime3_telo }
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prime5_telo
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.mix(prime3_telo)
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.mix(FIND_TELOMERE_REGIONS.out.telomere)
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.set { telo_for_extraction }
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} else {
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telo_for_extraction = FIND_TELOMERE_REGIONS.out.telomere
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}
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//
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// SUBWORKFLOW: TELO_EXTRACTION
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// - The prime5.mix(prime3) creates a queue channel to execute
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// TELO_EXTRACTION per item in channel
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//
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TELO_EXTRACTION (
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telo_for_extraction
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)
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ch_versions = ch_versions.mix( TELO_EXTRACTION.out.versions )
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TELO_EXTRACTION.out.bedgraph_file
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.map{ _meta, bedgraph ->
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bedgraph
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}
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.collect()
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.set { telo_bedgraphs }
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emit:
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bed_file = TELO_EXTRACTION.out.bed_file.collect() // Not used anymore
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bed_gz_tbi = TELO_EXTRACTION.out.bed_gz_tbi.collect() // Not used anymore
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bedgraph_file = telo_bedgraphs // Used in pretext_graph
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versions = ch_versions
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}

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