Removed custom seacr module (cea050cc) · Commits · Chaos / Cutandrun

modules/local/seacr_no_igg.nf

deleted100644 → 0

+0 −42

Original line number	Diff line number	Diff line
		include { initOptions; saveFiles; getSoftwareName } from './functions'

		params.options = [:]
		options = initOptions(params.options)

		def VERSION = '1.3'

		process SEACR_CALLPEAK {
		tag "$meta.id"
		label 'process_medium'
		publishDir "${params.outdir}",
		mode: params.publish_dir_mode,
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

		conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
		} else {
		container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
		}

		input:
		tuple val(meta), path(bedgraph)
		val (threshold)

		output:
		tuple val(meta), path("*.bed"), emit: bed
		path "*.version.txt" , emit: version

		script:
		def software = getSoftwareName(task.process)
		def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
		"""
		SEACR_1.3.sh \\
		$bedgraph \\
		$threshold \\
		$options.args \\
		$prefix

		echo $VERSION > ${software}.version.txt
		"""
		}

workflows/cutandrun.nf

+16 −11

Original line number	Diff line number	Diff line
		@@ -295,7 +295,6 @@ multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title
		include { INPUT_CHECK } from "../subworkflows/local/input_check" addParams( options: [:] )
		include { CAT_FASTQ } from "../modules/nf-core/modules/cat/fastq/main" addParams( options: cat_fastq_options )
		include { BEDTOOLS_GENOMECOV_SCALE } from "../modules/local/bedtools_genomecov_scale" addParams( options: modules["bedtools_genomecov_bedgraph"] )
		include { SEACR_CALLPEAK as SEACR_NO_IGG } from "../modules/local/seacr_no_igg" addParams( options: modules["seacr"] )
		include { AWK as AWK_NAME_PEAK_BED } from "../modules/local/awk" addParams( options: modules["awk_name_peak_bed"] )
		include { IGV_SESSION } from "../modules/local/igv_session" addParams( options: modules["igv"] )
		include { AWK as AWK_EDIT_PEAK_BED } from "../modules/local/awk" addParams( options: modules["awk_edit_peak_bed"] )
		@@ -336,6 +335,7 @@ include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META } from "../subworkflows
		include { UCSC_BEDCLIP } from "../modules/nf-core/modules/ucsc/bedclip/main" addParams( options: modules["ucsc_bedclip"] )
		include { UCSC_BEDGRAPHTOBIGWIG } from "../modules/nf-core/modules/ucsc/bedgraphtobigwig/main" addParams( options: modules["ucsc_bedgraphtobigwig"] )
		include { SEACR_CALLPEAK } from "../modules/nf-core/modules/seacr/callpeak/main" addParams( options: modules["seacr"] )
		include { SEACR_CALLPEAK as SEACR_CALLPEAK_NOIGG } from "../modules/nf-core/modules/seacr/callpeak/main" addParams( options: modules["seacr"] )
		include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE } from "../modules/nf-core/modules/deeptools/computematrix/main" addParams( options: modules["dt_compute_mat_gene"] )
		include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/modules/deeptools/computematrix/main" addParams( options: modules["dt_compute_mat_peaks"] )
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE } from "../modules/nf-core/modules/deeptools/plotheatmap/main" addParams( options: modules["dt_plotheatmap_gene"] )
		@@ -684,28 +684,33 @@ workflow CUTANDRUN {
		* MODULE: Call peaks with IgG control
		*/
		SEACR_CALLPEAK (
		ch_bedgraph_paired
		ch_bedgraph_paired,
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.version.first().ifEmpty(null))
		//ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.version.first().ifEmpty(null))
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_CALLPEAK.out.bed \| view
		}
		else {
		/*
		* CHANNEL: Load peak threshold into channel
		* CHANNEL: Add fake control channel
		*/
		ch_peak_threshold = Channel.value(params.peak_threshold)
		ch_bedgraph_split.target
		.map{ row-> [ row[0], row[1], [] ] }
		.set { ch_bedgraph_target_fctrl }
		// EXAMPLE CHANNEL STRUCT: [[META], BED, FAKE_CTRL]
		// ch_bedgraph_target_fctrl \| view

		/*
		* MODULE: Call peaks without IgG Control
		*/
		SEACR_NO_IGG (
		ch_bedgraph_split.target,
		ch_peak_threshold
		SEACR_CALLPEAK_NOIGG (
		ch_bedgraph_target_fctrl,
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_NO_IGG.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.version.first().ifEmpty(null))
		ch_seacr_bed = SEACR_CALLPEAK_NOIGG.out.bed
		//ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.version.first().ifEmpty(null))
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_NO_IGG.out.bed \| view
		}

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