name: picard_cleansam description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads keywords: - clean - sam - 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://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - sam: type: file description: SAM file pattern: "*.{sam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - sam: type: file description: Cleaned SAM file pattern: "*.{sam}" authors: - "@sateeshperi" - "@mjcipriano" - "@hseabolt"