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4efa8da5c5
* controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
50 lines
1.4 KiB
YAML
50 lines
1.4 KiB
YAML
name: controlfreec_assesssignificance
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description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC
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keywords:
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- cna
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- cnv
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- somatic
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- single
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- tumor-only
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tools:
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- controlfreec/assesssignificance:
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
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homepage: http://boevalab.inf.ethz.ch/FREEC
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documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
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tool_dev_url: https://github.com/BoevaLab/FREEC/
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doi: "10.1093/bioinformatics/btq635"
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licence: ["GPL >=2"]
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input:
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# Only when we have meta
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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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- cnvs:
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type: file
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description: _CNVs file generated by FREEC
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pattern: "*._CNVs"
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- ratio:
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type: file
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description: ratio file generated by FREEC
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pattern: "*.ratio.txt"
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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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- 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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- p_value_txt:
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type: file
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description: CNV file containing p_values for each call
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pattern: "*.p.value.txt"
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authors:
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- "@FriederikeHanssen"
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