name: fastqc description: Run FastQC on sequenced reads keywords: - Quality Control - QC - Adapters 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/ params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive 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. - options: type: map description: | Groovy Map containing module options for passing command-line arguments and output file paths. 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" - version: type: file description: File containing software version pattern: "*.version.txt" authors: - "@drpatelh" - "@grst" - "@ewels" - "@FelixKrueger"