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Parameter Docs
Sateesh Peri edited this page Mar 23, 2022
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CDCgov/mycosnp-nf v1.0dev
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Typical pipeline command:
nextflow run CDCgov/mycosnp-nf -profile singularity,test
Input/output options
--input [string] Path to comma-separated file containing information about the samples in the experiment.
--add_sra_file [string] Path to comma-separated file containing SRA ids to download from NCBI. Format: Name,SRAID
--add_vcf_file [string] Path to text file containing a list of file paths to vcf files generated from previous runs of this workflow to include
in this analysis. They must use the same exact reference. *.tbi file must be in same location. Text file with list in
Format: /path/to/vcf/file.gz
--outdir [string] Path to the output directory where the results will be saved. [default: ./results]
--publish_dir_mode [string] Method used to save pipeline results to output directory. [default: copy]
Reference genome options
--fasta [string] Path to FASTA formatted reference genome file.
--ref_dir [string] Path to reference genome masked files/picard dict/samtools fai/bwa index from previous run. If you use this command, it
invalidates `--fasta --ref_masked_fasta --ref_fai --ref_bwa --ref_dict`
--ref_masked_fasta [string] Path to reference genome masked fasta file. If you use this command, must provide all `--ref_masked_fasta --ref_fai
--ref_bwa --ref_dict`
--ref_fai [string] Path to reference genome samtools fai file. If you use this command, must provide all `--ref_masked_fasta --ref_fai
--ref_bwa --ref_dict`
--ref_dict [string] Path to reference genome picard tools dict file. If you use this command, must provide all `--ref_masked_fasta
--ref_fai --ref_bwa --ref_dict`
--ref_bwa [string] Path to reference genome bwatools bwa directory. If you use this command, must provide all `--ref_masked_fasta
--ref_fai --ref_bwa --ref_dict`
MycoSNP Run/Save/Skip Options
--save_reference [boolean] Saves the reference genome/index files to the results folder [default: true]
--save_alignment [boolean] Saves the reference alignment BAM files to the samples results folder [default: true]
--rapidnj [boolean] Build a tree using the RapidNJ neighbour-joining algorithm [default: true]
--fasttree [boolean] Build a tree using the FastTree approximate ML algorithm [default: true]
--iqtree [boolean] Build a tree using the IQ-TREE ML algorithm
--raxmlng [boolean] Build a tree using the RAxML-NG ML algorithm
--save_debug [boolean] Save intermediate files for debugging
--skip_samples [string] a comma separated list of IDs to skip for variant calling and analysis
--skip_samples_file [string] a file with new-line separated list of IDs to skip for variant calling and analysis
--skip_combined_analysis [boolean] Skip combined variant analysis (run reference prep and mapping)
--skip_phylogeny [boolean] Skip phylogenetic tree creation
MycoSNP Run Params
--sample_ploidy [integer] Ploidy of sample (GATK) [default: 1]
--coverage [integer] If coverage is specified and rate is not specified, coverage is used to calculate a down-sampling rate that results in
the specified coverage. For example if coverage 70, then FASTQ files are down-sampled such that, when aligned to the
reference, the result is approximately 70x coverage [default: 70]
--rate [number] If rate is specified, then coverage is ignored. rate specifies the rate for down-sampling FASTQ files. A rate of 1.0
indicates that 100% of reads in the FASTQ files are retained, which effectively "skips" down-sampling
--gvcfs_filter [string] Filter criteria for variants (GATK) [default: QD < 2.0 || FS > 60.0 || MQ < 40.0 || DP < 10]
--vcftools_filter [string] Filter criteria for VCFTOOLS [default: --min_GQ "50" --keep_GQ_0_refs --min_percent_alt_in_AD "0.8" --min_total_DP
"10" --keep_all_ref]
--max_amb_samples [integer] Max number of samples with ambiguous calls for inclusion (GATK) [default: 10000000]
--max_perc_amb_samples [integer] Max percent of samples with ambiguous calls for inclusion (GATK) [default: 10]
--mask [boolean] Perform masking of reference genome before analysis [default: true]
Generic options
--help [boolean] Display help text.
--tmpdir [string] temporary directory for shell and java processes [default: /tmp]