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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>
53 lines
1.3 KiB
YAML
53 lines
1.3 KiB
YAML
name: idr
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description: |
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Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible
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Discovery Rate)
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keywords:
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- IDR
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- peaks
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- ChIP-seq
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- ATAC-seq
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tools:
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- idr:
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description: |
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The IDR (Irreproducible Discovery Rate) framework is a unified approach
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to measure the reproducibility of findings identified from replicate
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experiments and provide highly stable thresholds based on reproducibility.
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homepage: None
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documentation: None
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tool_dev_url: https://github.com/kundajelab/idr
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doi: ""
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licence: ["GPL v2"]
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input:
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- peaks:
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type: tuple of two files
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description: BED, narrowPeak or broadPeak files of replicates
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pattern: "*"
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- peak_type:
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type: value
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description: Type of peak file
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pattern: "{narrowPeak,broadPeak,bed}"
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- prefix:
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type: value
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description: Prefix for output files
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output:
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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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- idr:
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type: file
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description: Text file containing IDR values
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pattern: "*.{txt}"
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- log:
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type: file
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description: Log file
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pattern: "*.{txt}"
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- png:
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type: file
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description: Plot generated by idr
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pattern: "*{.png}"
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authors:
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- "@drpatelh"
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- "@joseespinosa"
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