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"