Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
treatment_bam{:bash}
:file
Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates
*.{bam,sam}
control_bam{:bash}
:file
Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples
*.{bam,sam}
blacklist_bed{:bash}
:file
Bed file containing genomic intervals to exclude from the analysis
*.{bed}
Output
name:type
description
pattern
peak{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.narrowPeak{:bash}
:file
Narrow peak file containing genomic intervals of significant enrichment
*.{narrowPeak}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
bedgraph_pvalues{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.pvalues.bedGraph{:bash}
:file
bedGraph file containing p/q values
*.{pvalues.bedGraph}
bedgraph_pileup{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.pileup.bedGraph{:bash}
:file
bedGraph file containing pileups and p-values
*.{pileup.bedGraph}
bed_intervals{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.intervals.bed{:bash}
:file
Bed file containing annotated intervals
*.{intervals.bed}
duplicates{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.duplicates.txt{:bash}
:file
Text output file containing intervals corresponding to PCR duplicates
*.{intervals.txt}
Tools
genrich
MIT
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.
