name: picard_mergesamfiles description: Merges multiple BAM files into a single file keywords: - merge - alignment - bam - sam tools: - picard: description: | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ 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. - enable_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 ] - bam: type: file description: List of BAM files pattern: "*.{bam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: Merged BAM file pattern: "*.{bam}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@drpatelh"