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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
46 lines
1.5 KiB
YAML
46 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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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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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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