cwlVersion: v1.0 class: Workflow requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement expressionLib: - var get_root = function(basename) { return basename.split('.').slice(0,1).join('.'); }; inputs: alias: type: string label: "Experiment short name/Alias" sd:preview: position: 1 fastq_file: type: File label: "FASTQ file" format: "http://edamontology.org/format_1930" doc: "Reads data in a FASTQ format, optionally compressed" outputs: fastqc_report: type: File outputSource: rename_fastqc_report/target_file label: "FastqQC HTML report" doc: "FastqQC HTML report" steps: extract_fastq: run: ../tools/extract-fastq.cwl in: compressed_file: fastq_file out: [fastq_file] run_fastqc: run: ../tools/fastqc.cwl in: reads_file: extract_fastq/fastq_file out: - html_file rename_fastqc_report: run: ../tools/rename.cwl in: source_file: run_fastqc/html_file target_filename: source: fastq_file valueFrom: $(get_root(self.basename)+"_fastqc_report.html") out: [target_file] $namespaces: s: http://schema.org/ $schemas: - https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf s:name: "FastQC - a quality control tool for high throughput sequence data" label: "FastQC - a quality control tool for high throughput sequence data" s:alternateName: "FastQC - a quality control tool for high throughput sequence data" s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/fastqc.cwl s:codeRepository: https://github.com/datirium/workflows s:license: http://www.apache.org/licenses/LICENSE-2.0 s:isPartOf: class: s:CreativeWork s:name: Common Workflow Language s:url: http://commonwl.org/ s:creator: - class: s:Organization s:legalName: "Cincinnati Children's Hospital Medical Center" s:location: - class: s:PostalAddress s:addressCountry: "USA" s:addressLocality: "Cincinnati" s:addressRegion: "OH" s:postalCode: "45229" s:streetAddress: "3333 Burnet Ave" s:telephone: "+1(513)636-4200" s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" s:department: - class: s:Organization s:legalName: "Allergy and Immunology" s:department: - class: s:Organization s:legalName: "Barski Research Lab" s:member: - class: s:Person s:name: Michael Kotliar s:email: mailto:misha.kotliar@gmail.com s:sameAs: - id: http://orcid.org/0000-0002-6486-3898 # doc: # $include: ../descriptions/fastqc.md doc: | FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application