name: bwa_mem description: Performs fastq alignment to a fasta reference using BWA keywords: - mem - bwa - alignment - map - fastq - bam - sam 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 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. - index: type: file description: BWA genome index files pattern: "*.{amb,ann,bwt,pac,sa}" - fasta: type: file description: Input genome fasta file - options: type: map description: | Groovy Map containing module options for passing command-line arguments and output file paths. output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@drpatelh" - "@jeremy1805"