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* feat(bbmap): Initialize pileup module * test(bbmap): Update outputs * test(bbmap): Add pileup tags * style(bbmap): Add in when Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
47 lines
1.3 KiB
YAML
47 lines
1.3 KiB
YAML
name: "bbmap_pileup"
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description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
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keywords:
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- fasta
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- genome
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- coverage
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tools:
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- bbmap:
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description: BBMap is a short read aligner, as well as various other bioinformatic tools.
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homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
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tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
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doi: ""
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licence: ["UC-LBL license (see package)"]
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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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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,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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- stats:
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type: file
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description: Per-scaffold coverage info
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pattern: "*.stats.txt"
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- hist:
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type: file
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description: "Histogram of # occurrences of each depth level"
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pattern: "*.hist.txt"
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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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authors:
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- "@Emiller88"
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