nextflow run nf-core/eager -r dev \
           --pairedEnd \
           --reads 'data/Sample1/Sample1.pass_{1,2}.fastq.gz' \
           --fasta '/home/keaton/Reference/EAGER/rCRS/rCRS.fasta' \
           --bwa_index '/home/keaton/Reference/EAGER/rCRS/rCRS.fasta' \
           --fasta_index '/home/keaton/Reference/EAGER/rCRS/rCRS.fasta.fai' \
           --outdir output/ \
           --clip_readlength 35 \
           --clip_min_read_quality 0 \
           --clip_min_adap_overlap 3 \
           --bwaalnn 0.01 \
           --bwaalnl 16500 \
           --bam_mapping_quality_threshold 30 \
           --max_cpus 10 \
           --max_memory 64.G \
           --max_time 8.h \
           -name 'DedupTest_Run1'