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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
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: seacr_callpeak
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description: Call peaks using SEACR on sequenced reads in bedgraph format
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keywords:
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- peak-caller
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- peaks
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- bedgraph
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- cut&tag
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- cut&run
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- chromatin
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- seacr
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tools:
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- seacr:
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description: |
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SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
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or chromatin profiling data in which background is dominated by "zeroes"
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(i.e. regions with no read coverage).
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homepage: https://github.com/FredHutch/SEACR
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documentation: https://github.com/FredHutch/SEACR
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licence: ["GPL-2.0-only"]
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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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- bedgraph:
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type: file
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description: |
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The target bedgraph file from which the peaks will be calculated.
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- ctrlbedgraph:
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type: file
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description: |
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Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
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- threshold:
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type: value
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description: |
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Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
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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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- bed:
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type: file
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description: Bed file containing the calculated peaks.
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pattern: "*.bed"
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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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authors:
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- "@chris-cheshire"
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