name: picard_collectmultiplemetrics description: Collect multiple metrics from a BAM file keywords: - alignment - metrics - statistics - insert - quality - bam 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/ licence: ['MIT'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.{bam}" - fasta: type: file description: Genome fasta file output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - metrics: type: file description: Alignment metrics files generated by picard pattern: "*_{metrics}" - pdf: type: file description: PDF plots of metrics pattern: "*.{pdf}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh"