#!/bin/bash

/home/mdistefano/.conda/envs/eric_env_test/bin/nextflow run nf-core/crisprseq \
    --analysis screening \
    --input samplesheet.csv \
    --library library_correctformat.tsv \
    --outdir results \
    --aligner bowtie2 \
    --five_prime_adapter "GTTTTAG" \
    --three_prime_adapter "ACACCG" \
    --contrasts contrasts.csv \
    --rra \
    --genome GRCh38 \
    --save_trimmed \
    --save_reference \
    --read_length 100 \
    -r 2.3.0 \
    -c local.config \
    -resume \
    -with-trace \
    -with-report \
    -profile singularity