params.reads: Path to input reads in fastq format. Set as "[!*]" if none or when simulating reads.
params.bams: Path to aligned reads in bam format. Set as "[!*]" if none or when simulating reads.
params.ref: Path to reference genome fasta.
params.adapters: Path to adapter file. Can be empty when simulating reads.
params.pl: Platform. Ex: Illumina
params.pm: Machine: Ex: NextSeq
params.fcid: Unique name for this analysis (alphanumeric, no spaces)
params.outdir: Output path
params.do_sim_reads: true if simulating reads, else false.
params.mut_model_vcf: Path to VCF file to build mutation model
params.error_model_fq_read1: Read 1 of paired end fastq reads for error model
params.error_model_fq_read2: Read 2 of paired end fastq reads for error model
params.readsim_model_bam: Bam file for modeling
params.mut_rate: Mutation rate (between 0 and 0.3)
params.readsim_cov: Simulation coverage
params.m_rates: PCR error rates. Ex: 0.0005. This is an array with 2 elements, one for each PCR replicate. Do not change the length of this array or modify the "m1" or "m2" values. (Todo: get rid of this array and make this a single floating value parameter representing one error rate that will be applied to both PCR replicates)
params.seed: Random seed for PCR errors. This parameter ensures 'random' AF's between PCR replicates are equivilent.
params.readsim_downsample_fracs: Simulation downsampling fractions [random seed, fraction]
params.readsim_allele_fracs: Simulation allele frequencies. Accepts floating points values and 'random'
params.freebayes_configs, params.m2_configs, params.hc_configs, params.lofreq_configs, params.ivar_configs: Variant caller parameter configurations [name, params]
params.vs_configs, params.timo_configs: Variant caller parameter configurations including samtool configuration options [name, samtools params, variant caller params]
workDir: Nextflow workdir. Lots of temporary/intermediary files. Can delete once final analysis is complete.
process: Configuration for scheduler. Replace 'slurm' with execution scheduler. Resources required will vary greatly depending on input, however reasonable defaults have been provided by default.
Run the main.nf script, providing the path to the config, and specifying the -with-singularity parameter and the repo name:
module load nextflow/20.11.0-edge
nextflow run main.nf -c <path_to_config> -with-singularity gencorefacility/mad:2