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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>
48 lines
1.3 KiB
YAML
48 lines
1.3 KiB
YAML
name: homer_annotatepeaks
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description: Annotate peaks with HOMER suite
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keywords:
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- annotations
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- peaks
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- bed
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tools:
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- homer:
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description: |
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HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
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documentation: http://homer.ucsd.edu/homer/
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doi: 10.1016/j.molcel.2010.05.004.
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licence: ["GPL-3.0-or-later"]
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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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- peaks:
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type: file
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description: The peak files in bed format
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pattern: "*.bed"
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- fasta:
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type: file
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description: Fasta file of reference genome
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pattern: "*.fasta"
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- gtf:
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type: file
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description: GTF file of reference genome
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pattern: "*.gtf"
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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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- annotated_peaks:
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type: file
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description: The annotated peaks
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pattern: "*annotatePeaks.txt"
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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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- "@drpatelh"
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- "@kevinmenden"
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