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