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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
39 lines
1.1 KiB
YAML
39 lines
1.1 KiB
YAML
name: cooler_digest
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description: Generate fragment-delimited genomic bins
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keywords:
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- digest
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- enzyme
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tools:
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- cooler:
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description: Sparse binary format for genomic interaction matrices
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homepage: https://cooler.readthedocs.io/en/latest/index.html
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documentation: https://cooler.readthedocs.io/en/latest/index.html
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tool_dev_url: https://github.com/open2c/cooler
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doi: "10.1093/bioinformatics/btz540"
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licence: ["BSD-3-Clause"]
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input:
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- fasta:
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type: file
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description: Genome assembly FASTA file or folder containing FASTA files (uncompressed).
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pattern: "*.{fasta,fa}"
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- chromsizes:
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type: file
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description: Path to a chromsizes file.
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- enzyme:
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type: String
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description: Name of restriction enzyme. e.g. CviQI.
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documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html
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output:
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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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- bed:
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type: file
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description: A genome segmentation of restriction fragments as a BED file.
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pattern: "*.{bed}"
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authors:
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- "@jianhong"
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