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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
48 lines
1.2 KiB
YAML
48 lines
1.2 KiB
YAML
name: pairtools_parse
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description: Find ligation junctions in .sam, make .pairs
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keywords:
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- parse
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tools:
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- pairtools:
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description: CLI tools to process mapped Hi-C data
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homepage: http://pairtools.readthedocs.io/
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documentation: http://pairtools.readthedocs.io/
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tool_dev_url: https://github.com/mirnylab/pairtools
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doi: ""
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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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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- chromsizes:
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type: file
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description: chromosome size file
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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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- 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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- pairsam:
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type: file
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description: parsed pair file
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pattern: "*.{pairsam.gz}"
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- stat:
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type: file
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description: stats of the pairs
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pattern: "*.{pairsam.stat}"
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authors:
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- "@jianhong"
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