Initial release of nf-core/hicar pipeline.
Added
- Raw read QC (FastQC)
- Adapter trimming (cutadapt)
- Map and filter reads (bwa_mem, samtools, pairtools)
- Call peaks for ATAC (R2) reads (MACS2)
- Find genomic interactions and annotations (MAPS, ChIPpeakAnno)
- Differential analysis and annotations (edgeR, ChIPpeakAnno)
- Alignment QC metrics (samtools)
- ATAC R2 reads QC metrics (ATACseqQC)
- Pair QC metrics (pairsqc)
- Visualization (cooler, trackViewer, circos, ucsc_tools, bedtools, juicer_tools, igv.js)
- Collate and present various QC metrics (MultiQC)