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50 lines
1.4 KiB
YAML
50 lines
1.4 KiB
YAML
name: deeptools_bamcoverage
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description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
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keywords:
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- sort
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tools:
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- deeptools:
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description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
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homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
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documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
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tool_dev_url: https://github.com/deeptools/deepTools/
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doi: "https://doi.org/10.1093/nar/gkw257"
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licence: ["GPL v3"]
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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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- input:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAM/CRAM index file
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pattern: "*.{bai,crai}"
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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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- bigWig:
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type: file
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description: BigWig file
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pattern: "*.bigWig"
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- bedgraph:
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type: file
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description: Bedgraph file
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pattern: "*.bedgraph"
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authors:
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- "@FriederikeHanssen"
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