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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>
51 lines
1.8 KiB
YAML
51 lines
1.8 KiB
YAML
name: bedtools_genomecov
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description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
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keywords:
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- bed
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- bam
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- genomecov
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tools:
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- bedtools:
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description: |
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A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
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documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
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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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- intervals:
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type: file
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description: BAM/BED/GFF/VCF
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pattern: "*.{bam|bed|gff|vcf}"
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- scale:
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type: value
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description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
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- sizes:
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type: file
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description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
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- extension:
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type: string
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description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
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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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- genomecov:
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type: file
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description: Computed genome coverage file
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pattern: "*.${extension}"
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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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- "@sruthipsuresh"
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- "@drpatelh"
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- "@sidorov-si"
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- "@chris-cheshire"
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