#!/bin/env bash

set -x

nextflow run nf-core/cutandrun \
  -r 3.1 \
  -profile docker \
  --input /home/gng/cutandrun_h1_batch2/sample_sheet.csv \
  --outdir /home/gng/cutandrun_h1_batch2/output \
  --fasta /data/genomes/ncbi/GRCh38.analysisSet/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz \
  --bowtie2 /data/genomes/ncbi/GRCh38.analysisSet/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.bowtie_index.tar.gz \
  --gtf /data/genomes/ncbi/GRCh38.analysisSet/genes.gtf \
  --peakcaller 'macs2' \
  --skip_heatmaps true \
  --max_memory "400.GB"