diff --git a/nextflow.config b/nextflow.config index 9deef23f..48520b15 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,21 +20,21 @@ params { kraken2db = "" // Assembly parameters - assembler = 'unicycler' //allowed are unicycler, canu, miniasm - assembly_type = 'short' //allowed are short, long, hybrid (hybrid works only with Unicycler) + assembler = 'unicycler' // Allowed: ['unicycler', 'canu', 'miniasm'] + assembly_type = 'short' // Allowed: ['short', 'long', 'hybrid'] (hybrid works only with Unicycler) unicycler_args = "" - canu_mode = '-nanopore' // allowed modes: ["-pacbio", "-nanopore", "-pacbio-hifi"] - canu_args = '' //Default no extra options, can be adjusted by the user + canu_mode = '-nanopore' // Allowed: ['-pacbio', '-nanopore', '-pacbio-hifi'] + canu_args = '' // Default no extra options, can be adjusted by the user // Assembly polishing polish_method = 'medaka' // Annotation - annotation_tool = 'prokka' // allowed are 'prokka', 'bakta' or 'dfast' + annotation_tool = 'prokka' // Allowed: ['prokka', 'bakta','dfast'] prokka_args = "" baktadb = '' baktadb_download = false - baktadb_download_args = '--type light' // allowed: '--type light' or '--type full' + baktadb_download_args = '--type light' // Allowed: ['--type light', '--type full'] dfast_config = "$projectDir/assets/test_config_dfast.py" // Skipping options