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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>
47 lines
1.5 KiB
YAML
47 lines
1.5 KiB
YAML
name: bedtools_intersect
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description: Allows one to screen for overlaps between two sets of genomic features.
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keywords:
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- bed
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- intersect
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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/intersect.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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- intervals1:
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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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- intervals2:
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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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- extension:
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type: value
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description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
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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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- intersect:
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type: file
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description: File containing the description of overlaps found between the two features
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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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