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* add picard-cleansam * add picard/cleansam * update test yml with output * picard 2.26.10 -> 2.26.9 * add output to test yml Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
46 lines
1.2 KiB
YAML
46 lines
1.2 KiB
YAML
name: picard_cleansam
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description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
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keywords:
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- clean
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- sam
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- bam
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tools:
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- picard:
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description: |
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
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data and formats such as SAM/BAM/CRAM and VCF.
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homepage: https://broadinstitute.github.io/picard/
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documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard-
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tool_dev_url: https://github.com/broadinstitute/picard
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- sam:
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type: file
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description: SAM file
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pattern: "*.{sam}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- sam:
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type: file
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description: Cleaned SAM file
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pattern: "*.{sam}"
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authors:
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- "@sateeshperi"
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- "@mjcipriano"
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- "@hseabolt"
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