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* add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * simplify PR to analyze subcommand Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
55 lines
1.3 KiB
YAML
55 lines
1.3 KiB
YAML
name: pydamage_analyze
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description: Damage parameter estimation for ancient DNA
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keywords:
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- ancient DNA
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- aDNA
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- de novo assembly
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- filtering
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- damage
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- deamination
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- miscoding lesions
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- C to T
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- palaeogenomics
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- archaeogenomics
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- palaeogenetics
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- archaeogenetics
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tools:
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- pydamage:
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description: Damage parameter estimation for ancient DNA
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homepage: https://github.com/maxibor/pydamage
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documentation: https://pydamage.readthedocs.io/
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tool_dev_url: https://github.com/maxibor/pydamage
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licence: ['GPL v3']
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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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- bai:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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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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- csv:
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type: file
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description: PyDamage results as csv files
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pattern: "*.csv"
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authors:
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- "@maxibor"
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