diff --git a/software/SOFTWARE/TOOL/meta.yml b/software/SOFTWARE/TOOL/meta.yml index d8ae9a7d..5ce9a00d 100644 --- a/software/SOFTWARE/TOOL/meta.yml +++ b/software/SOFTWARE/TOOL/meta.yml @@ -1,42 +1,76 @@ -name: bwa mem -description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner +## TODO nf-core: Change the name of "software_tool" below +name: software_tool +## TODO nf-core: Add a description and keywords +description: Run FastQC on sequenced reads keywords: - - mem - - bwa - - alignment + - Quality Control + - QC + - Adapters tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://www.htslib.org/doc/samtools.html - arxiv: arXiv:1303.3997 + ## TODO nf-core: Change the name of "software_tool" below + - software_tool: + ## TODO nf-core: Add a description and other details for the tool below + 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/ +## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below +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 +## TODO nf-core: Add a description of all of the variables used as input input: - - - - id: - type: val - description: read/read pair id - - reads: - type: file - description: Input fastq file - pattern: "*.{fastq,fq}" - - index: - type: file - description: bwa indexes file - pattern: "*.{amb,ann,bwt,pac,sa}" - - prefix: - type: val - description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified. + - 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. +## TODO nf-core: Add a description of all of the variables used as output output: - - - - bam: - type: file - description: Output bam file - pattern: "*.bam" - - bamindex: - type: file - description: Output bam index file - pattern: "*.bai" - + - 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" +## TODO nf-core: Add your GitHub username below authors: - - "@jeremy1805" + - "@your_github_username"