nextflow run nf-core/eager -r dev \
           --pairedEnd \
           --reads 'data/*pass_{1,2}.fastq.gz' \
           --fasta 'reference/Enterobacteria_phage_lambda.fasta' \
           --bwa_index 'reference/Enterobacteria_phage_lambda.fasta' \
           --fasta_index 'reference/Enterobacteria_phage_lambda.fasta.fai' \
           --outdir output_devIndex/ \
           --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 5 \
           --max_time 8.h \
           -name 'IndexTest_devIndex_Run2' \