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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>
79 lines
2.5 KiB
YAML
79 lines
2.5 KiB
YAML
name: genrich
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description: Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
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keywords:
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- peak-calling
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- ChIP-seq
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- ATAC-seq
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tools:
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- genrich:
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description: |
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Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
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It analyzes alignment files generated following the assay and produces a file
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detailing peaks of significant enrichment.
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homepage: https://github.com/jsh58/Genrich
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documentation: https://github.com/jsh58/Genrich#readme
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tool_dev_url: https://github.com/jsh58/Genrich
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doi: ""
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licence: ["MIT"]
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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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- treatment_bam:
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type: file
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description: Coordinate sorted BAM/SAM file from treatment sample
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pattern: "*.{bam,sam}"
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- control_bam:
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type: file
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description: Coordinate sorted BAM/SAM file from control sample
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pattern: "*.{bam,sam}"
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- blacklist_bed:
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type: file
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description: Bed file containing genomic intervals to exclude from the analysis
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pattern: "*.{bed}"
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- save_pvalues:
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type: boolean
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description: Create bedgraph-ish file for p/q-values file
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- save_pileup:
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type: boolean
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description: Create bedgraph-ish file for pileups and p-values
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- save_bed:
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type: boolean
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description: Create BED file for reads/fragments/intervals
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- save_duplicates:
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type: boolean
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description: Create PCR duplicates file (only works if -r option is set)
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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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- peaks:
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type: file
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description: Output file is in ENCODE narrowPeak format
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pattern: "*.{narrowPeak}"
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- bedgraph_pvalues:
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type: file
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description: bedGraph file containing p/q values
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pattern: "*.{pvalues.bedGraph}"
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- bedgraph_pileup:
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type: file
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description: bedGraph file containing pileups and p-values
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pattern: "*.{pileup.bedGraph}"
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- bed_intervals:
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type: file
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description: Bed file containing annotated intervals
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pattern: "*.{intervals.bed}"
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- duplicates:
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type: file
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description: Text output file containing intervals corresponding to PCR duplicates
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pattern: "*.{intervals.txt}"
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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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authors:
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- "@JoseEspinosa"
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