Atacseq

nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq

sample,fastq_1,fastq_2,replicate
CONTROL,/path/to/ctrl_rep1_R1.fq.gz,/path/to/ctrl_rep1_R2.fq.gz,1
CONTROL,/path/to/ctrl_rep2_R1.fq.gz,/path/to/ctrl_rep2_R2.fq.gz,2
TREATMENT,/path/to/treat_rep1_R1.fq.gz,/path/to/treat_rep1_R2.fq.gz,1
TREATMENT,/path/to/treat_rep2_R1.fq.gz,/path/to/treat_rep2_R2.fq.gz,2

sample,condition
CONTROL,control
TREATMENT,treatment

nextflow run nf-core/atacseq -r 2.1.2 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 --read_length 50

--deseq2_design design.csv

results/
├── bwa/mergedLibrary/
│   ├── *.mLb.mkD.sorted.bam     # Filtered, deduplicated alignments
│   └── bigwig/
│       └── *.bigWig             # Coverage tracks
├── macs2/narrowPeak/
│   ├── *.narrowPeak             # Peak calls
│   └── consensus/
│       └── consensus_peaks.bed  # Merged peaks across replicates
├── deeptools/
│   ├── plotFingerprint/         # Library complexity
│   └── plotProfile/             # TSS enrichment
├── deseq2/                      # If --deseq2_design provided
└── multiqc/

library(ChIPseeker)
library(GenomicRanges)
peaks <- import("consensus_peaks.bed")
peakAnno <- annotatePeak(peaks, TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)

findMotifsGenome.pl consensus_peaks.bed hg38 motifs/ -size 200