art-illumina-pe

Simulate sequencing reads using ART (Illumina paired-end reads)

usage

nexus run --nf-workflow sequencing_simulation_art-illumina-pe.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_art "-l 150 -f 15 -ss HSXt -m 200 -s 10 -na"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fasta_file’.
--output_dir	Directory to which output files will be copied.
--params_art	art_illumina parameters (default: “-l 151 -f 15 -ss HSXt -m 200 -s 10”).