params.json

{
    "input": "/workspace/genepal/testdata/0.4.0/assemblysheet.csv",
    "protein_evidence": "/workspace/genepal/testdata/0.4.0/external-protein-fastas.txt",
    "eggnogmapper_db_dir": "/workspace/ComparativeDataSources/emapperdb/5.0.2",
    "eggnogmapper_tax_scope": 33090,
    "rna_evidence": "/workspace/genepal/testdata/0.4.0/rnasheet.csv",
    "liftoff_annotations": "/workspace/genepal/testdata/0.4.0/liftoffannotations.csv",
    "orthofinder_annotations": null,
    "outdir": "results",
    "email": null,
    "repeat_annotator": "repeatmodeler",
    "save_annotated_te_lib": false,
    "edta_is_sensitive": false,
    "repeatmasker_save_outputs": false,
    "fastqc_skip": true,
    "fastp_skip": false,
    "min_trimmed_reads": 10000,
    "fastp_extra_args": null,
    "save_trimmed": false,
    "remove_ribo_rna": false,
    "save_non_ribo_reads": false,
    "star_max_intron_length": 16000,
    "star_align_extra_args": null,
    "star_save_outputs": false,
    "save_cat_bam": false,
    "braker_extra_args": null,
    "liftoff_coverage": 0.9,
    "liftoff_identity": 0.9,
    "eggnogmapper_evalue": 0.00001,
    "eggnogmapper_pident": 35,
    "allow_isoforms": true,
    "enforce_full_intron_support": true,
    "filter_liftoff_by_hints": true,
    "eggnogmapper_purge_nohits": false,
    "braker_save_outputs": false,
    "add_attrs_to_proteins_fasta": false,
    "busco_skip": false,
    "busco_lineage_datasets": "embryophyta_odb10"
}