Moved trimgalore to custom module (e0f31a5c) · Commits · Chaos / Cutandrun

modules.json

+0 −3

Original line number	Diff line number	Diff line
		@@ -54,9 +54,6 @@
		"seacr/callpeak": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},
		"trimgalore": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		},
		"ucsc/bedclip": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},

modules/local/modules/trimgalore/main.nf

+25 −12

Original line number	Diff line number	Diff line
		@@ -11,18 +11,18 @@ process TRIMGALORE {
		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::trim-galore=0.6.7' : null)
		conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
		container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
		} else {
		container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
		container "quay.io/biocontainers/trim-galore:0.6.6--0"
		}

		input:
		tuple val(meta), path(reads)

		output:
		tuple val(meta), path("*.fq.gz") , emit: reads
		tuple val(meta), path("*trimmed.fastq.gz") , emit: reads
		tuple val(meta), path("*report.txt") , emit: log
		path "*.version.txt" , emit: version

		@@ -49,7 +49,11 @@ process TRIMGALORE {

		// Added soft-links to original fastqs for consistent naming in MultiQC
		def software = getSoftwareName(task.process)
		def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
		def suffix = options.suffix ? "${options.suffix}.trimmed" : ".trimmed"
		def prefix_1 = "${meta.id}_1${suffix}"
		def prefix_2 = "${meta.id}_2${suffix}"
		def prefix = "${meta.id}${suffix}"

		if (meta.single_end) {
		"""
		[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
		@@ -64,8 +68,8 @@ process TRIMGALORE {
		"""
		} else {
		"""
		[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
		[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
		[ ! -f ${meta.id}_1.fastq.gz ] && ln -s ${reads[0]} ${meta.id}_1.fastq.gz
		[ ! -f ${meta.id}_2.fastq.gz ] && ln -s ${reads[1]} ${meta.id}_2.fastq.gz
		trim_galore \\
		$options.args \\
		--cores $cores \\
		@@ -75,9 +79,18 @@ process TRIMGALORE {
		$c_r2 \\
		$tpc_r1 \\
		$tpc_r2 \\
		${prefix}_1.fastq.gz \\
		${prefix}_2.fastq.gz
		${meta.id}_1.fastq.gz \\
		${meta.id}_2.fastq.gz
		echo \$(trim_galore --version 2>&1) \| sed 's/^.version //; s/Last.\$//' > ${software}.version.txt

		mv ${meta.id}_1_val_1.fq.gz ${prefix_1}.fastq.gz
		mv ${meta.id}_2_val_2.fq.gz ${prefix_2}.fastq.gz

		[ ! -f ${meta.id}_1_val_1_fastqc.html ] \|\| mv ${meta.id}_1_val_1_fastqc.html ${meta.id}_1_fastqc${suffix}.html
		[ ! -f ${meta.id}_2_val_2_fastqc.html ] \|\| mv ${meta.id}_2_val_2_fastqc.html ${meta.id}_2_fastqc${suffix}.html

		[ ! -f ${meta.id}_1_val_1_fastqc.zip ] \|\| mv ${meta.id}_1_val_1_fastqc.zip ${meta.id}_1_fastqc${suffix}.zip
		[ ! -f ${meta.id}_2_val_2_fastqc.zip ] \|\| mv ${meta.id}_2_val_2_fastqc.zip ${meta.id}_2_fastqc${suffix}.zip
		"""
		}
		}
		No newline at end of file

modules/nf-core/modules/trimgalore/meta.yml

deleted100644 → 0

+0 −58

Original line number	Diff line number	Diff line
		name: trimgalore
		description: Trim FastQ files using Trim Galore!
		keywords:
		- trimming
		- adapters
		- sequencing adapters
		- fastq
		tools:
		- trimgalore:
		description: \|
		A wrapper tool around Cutadapt and FastQC to consistently apply quality
		and adapter trimming to FastQ files, with some extra functionality for
		MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
		homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
		documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
		input:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- reads:
		type: file
		description: \|
		List of input FastQ files of size 1 and 2 for single-end and paired-end data,
		respectively.
		output:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- reads:
		type: file
		description: \|
		List of input adapter trimmed FastQ files of size 1 and 2 for
		single-end and paired-end data, respectively.
		pattern: "*.{fq.gz}"
		- html:
		type: file
		description: FastQC report (optional)
		pattern: "*_{fastqc.html}"
		- zip:
		type: file
		description: FastQC report archive (optional)
		pattern: "*_{fastqc.zip}"
		- log:
		type: file
		description: Trim Galore! trimming report
		pattern: "*_{report.txt}"
		- version:
		type: file
		description: File containing software version
		pattern: "*.{version.txt}"
		authors:
		- "@drpatelh"
		- "@ewels"
		- "@FelixKrueger"

subworkflows/nf-core/fastqc_trimgalore.nf→subworkflows/local/fastqc_trimgalore.nf

+2 −2

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ params.fastqc_options = [:]
		params.trimgalore_options = [:]

		include { FASTQC } from '../../modules/nf-core/modules/fastqc/main' addParams( options: params.fastqc_options )
		include { TRIMGALORE } from '../../modules/nf-core/modules/trimgalore/main' addParams( options: params.trimgalore_options )
		include { TRIMGALORE } from '../../modules/local/modules/trimgalore/main' addParams( options: params.trimgalore_options )

		workflow FASTQC_TRIMGALORE {
		take:

workflows/cutandrun.nf

+12 −12

Original line number	Diff line number	Diff line
		@@ -306,6 +306,7 @@ include { CONSENSUS_PEAKS } from "../subworkflow
		include { CONSENSUS_PEAKS as CONSENSUS_PEAKS_ALL } from "../subworkflows/local/consensus_peaks" addParams( bedtools_merge_options: modules["bedtools_merge_groups"], sort_options: modules["sort_group_peaks"], awk_threshold_options: awk_all_threshold, plot_peak_options: modules["plot_peaks"], run_peak_plotting: run_peak_plotting)
		include { ANNOTATE_META_AWK as ANNOTATE_DEDUP_META } from "../subworkflows/local/annotate_meta_awk" addParams( options: awk_dedup_options, meta_suffix: "", meta_prefix: "dedup_", script_mode: false )
		include { CALCULATE_FRAGMENTS } from "../subworkflows/local/calculate_fragments" addParams( samtools_options: modules["calc_frag_samtools"], samtools_view_options: modules["calc_frag_samtools_view"], bamtobed_options: modules["calc_frag_bamtobed"], awk_options: modules["calc_frag_awk"], cut_options: modules["calc_frag_cut"] )
		include { FASTQC_TRIMGALORE } from "../subworkflows/local/fastqc_trimgalore" addParams( fastqc_options: modules["fastqc"], trimgalore_options: trimgalore_options )

		/*
		========================================================================================
		@@ -329,7 +330,6 @@ include { SAMTOOLS_INDEX } from "../mo
		/*
		* SUBWORKFLOW: Consisting entirely of nf-core/modules
		*/
		include { FASTQC_TRIMGALORE } from "../subworkflows/nf-core/fastqc_trimgalore" addParams( fastqc_options: modules["fastqc"], trimgalore_options: trimgalore_options )
		include { MARK_DUPLICATES_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard" addParams( markduplicates_options: picard_markduplicates_options, samtools_options: picard_markduplicates_samtools_options, control_only: false )
		include { MARK_DUPLICATES_PICARD as DEDUP_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard" addParams( markduplicates_options: picard_deduplicates_options, samtools_options: picard_deduplicates_samtools_options, control_only: dedup_control_only )

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