diff --git a/conf/test_cobra.config b/conf/test_cobra.config new file mode 100644 index 00000000..e7afd881 --- /dev/null +++ b/conf/test_cobra.config @@ -0,0 +1,33 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/phageannotator -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Test COBRA profile' + config_profile_description = 'Minimal test dataset to check COBRA function ' + + // Limit resources so that this can run on GitHub Actions + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + + // Input data + input = 'https://github.com/nf-core/test-datasets/raw/phageannotator/assets/1.0.0/test_samplesheet.csv' + + // Tool options + run_cobra = true + cobra_assembler = 'megahit' + cobra_mink = 21 + cobra_maxk = 141 + + // Pipeline options + publish_dir_mode = 'symlink' +} diff --git a/nextflow_schema.json b/nextflow_schema.json index dc4a29b2..6f5b931b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -152,14 +152,15 @@ }, "cobra_assembler": { "type": "string", - "description": "The assembler that was used to assemble viral contigs" + "description": "The assembler that was used to assemble viral contigs", + "enum": ["idba", "metaspades", "megahit"] }, "cobra_mink": { - "type": "string", + "type": "integer", "description": "Minimum kmer value used during assembly" }, "cobra_maxk": { - "type": "string", + "type": "integer", "description": "Maximum kmer value used during assembly" } }