Parameter Docs

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  nf-core/mycosnp v1.0dev
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Typical pipeline command:

  nextflow run main.nf --input samplesheet.csv -profile singularity

Input/output options
  --input                      [string]  Path to comma-separated file containing information about the samples in the experiment.
  --outdir                     [string]  Path to the output directory where the results will be saved. [default: ./results]
  --email                      [string]  Email address for completion summary.
  --multiqc_title              [string]  MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Reference genome options
  --genome                     [string]  Name of iGenomes reference.
  --fasta                      [string]  Path to FASTA genome file.

Other parameters
  --save_reference             [string]  null [default: true]
  --save_alignment             [string]  null [default: true]
  --sample_ploidy              [integer] null [default: 1]
  --coverage                   [integer] null [default: 70]
  --rate                       [string]  null [default: ]
  --gvcfs_filter               [string]  null [default: QD < 2.0 || FS > 60.0 || MQ < 40.0 || DP < 10]
  --vcftools_filter            [string]  null [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] null [default: 10000000]
  --max_perc_amb_samples       [integer] null [default: 10]
  --publish_dir_mode           [string]  null [default: symlink]
  --rapidnj                    [string]  null [default: true]
  --fasttree                   [string]  null [default: true]
  --iqtree                     [string]  null [default: true]
  --raxmlng                    [string]  null [default: true]
  --save_debug                 [string]  null [default: false]
  --mask                       [string]  null [default: true]
  --tmpdir                     [string]  null [default: /tmp]
  --skip_samples               [string]  null [default: ]
  --skip_samples_file          [string]  null
  --skip_vcf                   [string]  null [default: false]