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| process FASTQC { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
|
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||
| conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : | ||
| 'biocontainers/fastqc:0.11.9--0' }" | ||
|
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||
| input: | ||
| tuple val(meta), path(reads) | ||
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||
| output: | ||
| tuple val(meta), path("*.html"), emit: html | ||
| tuple val(meta), path("*.zip") , emit: zip | ||
| path "versions.yml" , emit: versions | ||
|
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||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| def args = task.ext.args ?: '' | ||
| // Add soft-links to original FastQs for consistent naming in pipeline | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| if (meta.single_end) { | ||
| """ | ||
| [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz | ||
| fastqc $args --threads $task.cpus ${prefix}.fastq.gz | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) | ||
| END_VERSIONS | ||
| """ | ||
| } 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 | ||
| fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) | ||
| END_VERSIONS | ||
| """ | ||
| } | ||
|
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.html | ||
| touch ${prefix}.zip | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| name: fastqc | ||
| description: Run FastQC on sequenced reads | ||
| keywords: | ||
| - quality control | ||
| - qc | ||
| - adapters | ||
| - fastq | ||
| tools: | ||
| - fastqc: | ||
| description: | | ||
| FastQC gives general quality metrics about your reads. | ||
| It provides information about the quality score distribution | ||
| across your reads, the per base sequence content (%A/C/G/T). | ||
| You get information about adapter contamination and other | ||
| overrepresented sequences. | ||
| homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | ||
| documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ | ||
| licence: ["GPL-2.0-only"] | ||
| 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 ] | ||
| - html: | ||
| type: file | ||
| description: FastQC report | ||
| pattern: "*_{fastqc.html}" | ||
| - zip: | ||
| type: file | ||
| description: FastQC report archive | ||
| pattern: "*_{fastqc.zip}" | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@drpatelh" | ||
| - "@grst" | ||
| - "@ewels" | ||
| - "@FelixKrueger" |
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| process MULTIQC { | ||
| label 'process_medium' | ||
|
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||
| conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : | ||
| 'biocontainers/multiqc:1.12--pyhdfd78af_0' }" | ||
|
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| input: | ||
| path multiqc_files, stageAs: "?/*" | ||
| tuple path(multiqc_config), path(multiqc_logo) | ||
|
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| output: | ||
| path "*multiqc_report.html", emit: report | ||
| path "*_data" , emit: data | ||
| path "*_plots" , optional:true, emit: plots | ||
| path "versions.yml" , emit: versions | ||
|
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| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def config = multiqc_config ? "--config $multiqc_config" : '' | ||
| """ | ||
| multiqc \\ | ||
| --force \\ | ||
| $config \\ | ||
| $args \\ | ||
| . | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) | ||
| END_VERSIONS | ||
| """ | ||
|
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||
| stub: | ||
| """ | ||
| touch multiqc_data | ||
| touch multiqc_plots | ||
| touch multiqc_report.html | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| name: MultiQC | ||
| description: Aggregate results from bioinformatics analyses across many samples into a single report | ||
| keywords: | ||
| - QC | ||
| - bioinformatics tools | ||
| - Beautiful stand-alone HTML report | ||
| tools: | ||
| - multiqc: | ||
| description: | | ||
| MultiQC searches a given directory for analysis logs and compiles a HTML report. | ||
| It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. | ||
| homepage: https://multiqc.info/ | ||
| documentation: https://multiqc.info/docs/ | ||
| licence: ["GPL-3.0-or-later"] | ||
| input: | ||
| - multiqc_files: | ||
| type: file | ||
| description: | | ||
| List of reports / files recognised by MultiQC, for example the html and zip output of FastQC | ||
| - multiqc_config: | ||
| type: file | ||
| description: Config yml for MultiQC | ||
| pattern: "*.{yml,yaml}" | ||
| - multiqc_logo: | ||
| type: file | ||
| description: Logo file for MultiQC | ||
| pattern: "*.{png}" | ||
| output: | ||
| - report: | ||
| type: file | ||
| description: MultiQC report file | ||
| pattern: "multiqc_report.html" | ||
| - data: | ||
| type: directory | ||
| description: MultiQC data dir | ||
| pattern: "multiqc_data" | ||
| - plots: | ||
| type: file | ||
| description: Plots created by MultiQC | ||
| pattern: "*_data" | ||
| - versions: | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@abhi18av" | ||
| - "@bunop" | ||
| - "@drpatelh" |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "title": "Meta yaml", | ||
| "description": "Validate the meta yaml file for an nf-core module", | ||
| "type": "object", | ||
| "properties": { | ||
| "name": { | ||
| "type": "string", | ||
| "description": "Name of the module" | ||
| }, | ||
| "description": { | ||
| "type": "string", | ||
| "description": "Description of the module" | ||
| }, | ||
| "keywords": { | ||
| "type": "array", | ||
| "description": "Keywords for the module", | ||
| "items": { | ||
| "type": "string" | ||
| }, | ||
| "minItems": 3 | ||
| }, | ||
| "authors": { | ||
| "type": "array", | ||
| "description": "Authors of the module", | ||
| "items": { | ||
| "type": "string" | ||
| } | ||
| }, | ||
| "input": { | ||
| "type": "array", | ||
| "description": "Input channels for the module", | ||
|
|
||
| "items": { | ||
| "type": "object", | ||
| "patternProperties": { | ||
| ".*": { | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { | ||
| "type": "string", | ||
| "description": "Type of the input channel", | ||
| "enum": ["map", "file", "directory", "string", "integer", "float"] | ||
| }, | ||
| "description": { | ||
| "type": "string", | ||
| "description": "Description of the input channel" | ||
| }, | ||
| "pattern": { | ||
| "type": "string", | ||
| "description": "Pattern of the input channel, given in Java glob syntax" | ||
| }, | ||
| "default": { | ||
| "type": ["string", "number", "boolean", "array", "object"], | ||
| "description": "Default value for the input channel" | ||
| } | ||
| }, | ||
| "required": ["type", "description"] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "output": { | ||
| "type": "array", | ||
| "description": "Output channels for the module", | ||
| "items": { | ||
| "type": "object", | ||
| "patternProperties": { | ||
| ".*": { | ||
| "type": "object", | ||
| "properties": { | ||
| "type": { | ||
| "type": "string", | ||
| "description": "Type of the output channel", | ||
| "enum": ["map", "file", "directory", "string", "integer", "float"] | ||
| }, | ||
| "description": { | ||
| "type": "string", | ||
| "description": "Description of the output channel" | ||
| }, | ||
| "pattern": { | ||
| "type": "string", | ||
| "description": "Pattern of the input channel, given in Java glob syntax" | ||
| } | ||
| }, | ||
| "required": ["type", "description"] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "tools": { | ||
| "type": "array", | ||
| "description": "Tools used by the module", | ||
| "items": { | ||
| "type": "object", | ||
| "patternProperties": { | ||
| ".*": { | ||
| "type": "object", | ||
| "properties": { | ||
| "description": { | ||
| "type": "string", | ||
| "description": "Description of the output channel" | ||
| }, | ||
| "homepage": { | ||
| "type": "string", | ||
| "description": "Homepage of the tool", | ||
| "pattern": "^(http|https)://.*$" | ||
| }, | ||
| "documentation": { | ||
| "type": "string", | ||
| "description": "Documentation of the tool", | ||
| "pattern": "^(http|https)://.*$" | ||
| }, | ||
| "tool_dev_url": { | ||
| "type": "string", | ||
| "description": "URL of the development version of the tool's documentation", | ||
| "pattern": "^(http|https)://.*$" | ||
| }, | ||
| "doi": { | ||
| "type": "string", | ||
| "description": "DOI of the tool", | ||
| "pattern": "^10.\\d{4,9}\\/[^,]+$" | ||
| }, | ||
| "licence": { | ||
| "type": ["array", "string"], | ||
| "description": "Licence of the tool", | ||
| "items": { | ||
| "type": "string" | ||
| }, | ||
| "uniqueItems": true | ||
| } | ||
| }, | ||
| "required": ["description"], | ||
| "anyOf": [ | ||
| { "required": ["homepage"] }, | ||
| { "required": ["documentation"] }, | ||
| { "required": ["tool_dev_url"] }, | ||
| { "required": ["doi"] } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "required": ["name", "description", "keywords", "authors", "output", "tools"] | ||
| } |