Parameters - jacksonhturner/orthogarden GitHub Wiki

Parameters

When calling Orthogarden, in addition to the nextflow run command, you'll want to understand the necessary pipeline parameters. Note that all user parameters listed here must begin with -- (dash dash).

Necessary Parameters

parameter type description
--publish-dir path Where work and output files are stored. See Accessing & Interpreting Output.
--input path This must reference a comma-separated metadata file with the structure provided .
--augustus-ref string Augustus reference identifier to annotate assemblies. Species lists here and here.

Example (assuming results directory is where you want output and orthogarden is cloned to your $HOME directory):

nextflow run ~/orthogarden/main.nf \
    --publish-dir results \
    --input metadata.csv \
    --augustus-ref "aedes"

Optional Parameters

parameter type description default
--kraken_db path Kraken2 database of non-target sequences to filter such as these. false
--skip_qc bool Skip the FastQC and MultiQC steps of this pipeline. true
--skip-kraken bool Skip the kraken2 step of this pipeline. true
--skip_trim bool Skip trimming steps true
--r1_adapter string The R1 adapter sequence. Requires --skip_trim false. false
--r2_adapter string The R2 adapter sequence. Requires --skip_trim false. false
--minimum-length int Discard reads of this length in bp or less. Requires --skip_trim true. 30
--buffer-n int Use n files/batch for multi-gene processing steps 500
--threshold_val float The threshold of OrthoFinder genes existing as SCG (0 to 1) 0.9
--masking-threshold float This is the proportion of missing data required for masking (0 to 1). 0.4
--retain-third_pos bool Include third codon positions in your phylogeny. true
--ulimit int Maximum file limit for OrthoFinder step 100000
⚠️ **GitHub.com Fallback** ⚠️