Loading modules/nf-core/modules/trimgalore/functions.nf +68 −59 Original line number Diff line number Diff line /* * ----------------------------------------------------- * Utility functions used in nf-core DSL2 module files * ----------------------------------------------------- */ // // Utility functions used in nf-core DSL2 module files // /* * Extract name of software tool from process name using $task.process */ // // Extract name of software tool from process name using $task.process // def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } /* * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules */ // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // def initOptions(Map args) { def Map options = [:] options.args = args.args ?: '' options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false options.args3 = args.args3 ?: '' options.publish_by_meta = args.publish_by_meta ?: [] options.publish_dir = args.publish_dir ?: '' options.publish_files = args.publish_files options.suffix = args.suffix ?: '' return options } /* * Tidy up and join elements of a list to return a path string */ // // Tidy up and join elements of a list to return a path string // def getPathFromList(path_list) { def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes return paths.join('/') } /* * Function to save/publish module results */ // // Function to save/publish module results // def saveFiles(Map args) { if (!args.filename.endsWith('.version.txt')) { def ioptions = initOptions(args.options) def path_list = [ ioptions.publish_dir ?: args.publish_dir ] if (ioptions.publish_by_id) { path_list.add(args.publish_id) if (ioptions.publish_by_meta) { def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta for (key in key_list) { if (args.meta && key instanceof String) { def path = key if (args.meta.containsKey(key)) { path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } path = path instanceof String ? path : '' path_list.add(path) } } } if (ioptions.publish_files instanceof Map) { for (ext in ioptions.publish_files) { Loading modules/nf-core/modules/trimgalore/main.nf +12 −25 Original line number Diff line number Diff line Loading @@ -11,18 +11,18 @@ process TRIMGALORE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null) conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0" container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0" } else { container "quay.io/biocontainers/trim-galore:0.6.6--0" container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0" } input: tuple val(meta), path(reads) output: tuple val(meta), path("*trimmed.fastq.gz") , emit: reads tuple val(meta), path("*.fq.gz") , emit: reads tuple val(meta), path("*report.txt"), emit: log path "*.version.txt" , emit: version Loading @@ -49,11 +49,7 @@ process TRIMGALORE { // Added soft-links to original fastqs for consistent naming in MultiQC def software = getSoftwareName(task.process) def suffix = options.suffix ? "${options.suffix}.trimmed" : ".trimmed" def prefix_1 = "${meta.id}_1${suffix}" def prefix_2 = "${meta.id}_2${suffix}" def prefix = "${meta.id}${suffix}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz Loading @@ -68,8 +64,8 @@ process TRIMGALORE { """ } else { """ [ ! -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 [ ! -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 trim_galore \\ $options.args \\ --cores $cores \\ Loading @@ -79,18 +75,9 @@ process TRIMGALORE { $c_r2 \\ $tpc_r1 \\ $tpc_r2 \\ ${meta.id}_1.fastq.gz \\ ${meta.id}_2.fastq.gz ${prefix}_1.fastq.gz \\ ${prefix}_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 """ } } modules/nf-core/modules/trimgalore/meta.yml +0 −41 Original line number Diff line number Diff line Loading @@ -13,47 +13,6 @@ tools: 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 params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/<SOFTWARE>` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - enable_conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. - clip_r1: type: integer description: | Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads) - clip_r2: type: integer description: | Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only) - three_prime_clip_r1: type: integer description: | Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed - three_prime_clip_r2: type: integer description: | Instructs Trim Galore to re move bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed input: - meta: type: map Loading Loading
modules/nf-core/modules/trimgalore/functions.nf +68 −59 Original line number Diff line number Diff line /* * ----------------------------------------------------- * Utility functions used in nf-core DSL2 module files * ----------------------------------------------------- */ // // Utility functions used in nf-core DSL2 module files // /* * Extract name of software tool from process name using $task.process */ // // Extract name of software tool from process name using $task.process // def getSoftwareName(task_process) { return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() } /* * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules */ // // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // def initOptions(Map args) { def Map options = [:] options.args = args.args ?: '' options.args2 = args.args2 ?: '' options.publish_by_id = args.publish_by_id ?: false options.args3 = args.args3 ?: '' options.publish_by_meta = args.publish_by_meta ?: [] options.publish_dir = args.publish_dir ?: '' options.publish_files = args.publish_files options.suffix = args.suffix ?: '' return options } /* * Tidy up and join elements of a list to return a path string */ // // Tidy up and join elements of a list to return a path string // def getPathFromList(path_list) { def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes return paths.join('/') } /* * Function to save/publish module results */ // // Function to save/publish module results // def saveFiles(Map args) { if (!args.filename.endsWith('.version.txt')) { def ioptions = initOptions(args.options) def path_list = [ ioptions.publish_dir ?: args.publish_dir ] if (ioptions.publish_by_id) { path_list.add(args.publish_id) if (ioptions.publish_by_meta) { def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta for (key in key_list) { if (args.meta && key instanceof String) { def path = key if (args.meta.containsKey(key)) { path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] } path = path instanceof String ? path : '' path_list.add(path) } } } if (ioptions.publish_files instanceof Map) { for (ext in ioptions.publish_files) { Loading
modules/nf-core/modules/trimgalore/main.nf +12 −25 Original line number Diff line number Diff line Loading @@ -11,18 +11,18 @@ process TRIMGALORE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null) conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0" container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0" } else { container "quay.io/biocontainers/trim-galore:0.6.6--0" container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0" } input: tuple val(meta), path(reads) output: tuple val(meta), path("*trimmed.fastq.gz") , emit: reads tuple val(meta), path("*.fq.gz") , emit: reads tuple val(meta), path("*report.txt"), emit: log path "*.version.txt" , emit: version Loading @@ -49,11 +49,7 @@ process TRIMGALORE { // Added soft-links to original fastqs for consistent naming in MultiQC def software = getSoftwareName(task.process) def suffix = options.suffix ? "${options.suffix}.trimmed" : ".trimmed" def prefix_1 = "${meta.id}_1${suffix}" def prefix_2 = "${meta.id}_2${suffix}" def prefix = "${meta.id}${suffix}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz Loading @@ -68,8 +64,8 @@ process TRIMGALORE { """ } else { """ [ ! -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 [ ! -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 trim_galore \\ $options.args \\ --cores $cores \\ Loading @@ -79,18 +75,9 @@ process TRIMGALORE { $c_r2 \\ $tpc_r1 \\ $tpc_r2 \\ ${meta.id}_1.fastq.gz \\ ${meta.id}_2.fastq.gz ${prefix}_1.fastq.gz \\ ${prefix}_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 """ } }
modules/nf-core/modules/trimgalore/meta.yml +0 −41 Original line number Diff line number Diff line Loading @@ -13,47 +13,6 @@ tools: 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 params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/<SOFTWARE>` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - enable_conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. - clip_r1: type: integer description: | Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads) - clip_r2: type: integer description: | Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only) - three_prime_clip_r1: type: integer description: | Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed - three_prime_clip_r2: type: integer description: | Instructs Trim Galore to re move bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed input: - meta: type: map Loading
