Modify input parameters to integrate with IRIDA-Next UI

assets/schema_input.json

@@ -15,6 +15,7 @@
             },
             "contigs": {
                 "type": "string",
+                "format": "file-path",
                 "pattern": "^\\S+\\.f(ast|n)?a\\.gz$",
                 "errorMessage": "FASTA file containing assembled contigs, cannot contain spaces and must have extension '.fa.gz' or '.fasta.gz'"
             },

conf/modules.config

@@ -50,6 +50,18 @@ process {
         def point_db_arg = {String database -> " --pointfinder-organism ${database} " }
         def plasmid_db_arg = {String database -> " --plasmidfinder-database-type ${database} " }
         def mlst_arg = {String scheme -> " --mlst-scheme ${scheme} " }
+        def minimum_contig_length_arg = {String min_length -> " --minimum-contig-length ${min_length} "}
+        def genome_size_lower_bound_arg = {String min_genome -> " --genome-size-lower-bound ${min_genome} "}
+        def genome_size_upper_bound_arg = {String max_genome -> " --genome-size-upper-bound ${max_genome} "}
+        def minimum_N50_value_arg = {String min_n50 -> " --minimum-N50-value ${min_n50} "}
+        def unacceptable_number_contigs_arg = {String min_length -> " --unacceptable-number-contigs ${min_length} "}
+        def pid_threshold_arg = {String min_pid -> " --pid-threshold ${min_pid} "}
+        def percent_length_overlap_plasmidfinder_arg = {String min_overlap -> " --percent-length-overlap-plasmidfinder ${min_overlap} "}
+        def percent_length_overlap_resfinder_arg = {String min_overlap -> " --percent-length-overlap-resfinder ${min_overlap} "}
+        def percent_length_overlap_pointfinder_arg = {String min_overlap -> " --percent-length-overlap-pointfinder ${min_overlap} "}
+        def no_exclude_genes_arg = " --no-exclude-genes"
+        def exclude_negatives_arg = " --exclude-negatives"
+        def exclude_resistance_phenotypes_arg = " --exclude-resistance-phenotypes"
 
         // Check to see if the database name is valid:
         def valid_point_db = {String database -> pointfinder_databases.contains(database)}
@@ -58,8 +70,8 @@ process {
         ext.args = {
             [
                 // Pointfinder database:
-                params.pointfinder_database && valid_point_db(params.pointfinder_database) ?
-                    point_db_arg(params.pointfinder_database) :
+                params.pointfinder_database && valid_point_db(convert(params.pointfinder_database)) ?
+                    point_db_arg(convert(params.pointfinder_database)) :
                         meta.species && valid_point_db(convert(meta.species)) ?
                             point_db_arg(convert(meta.species)) : "",
 
@@ -68,8 +80,48 @@ process {
                     ? plasmid_db_arg(params.plasmidfinder_database) : "",
 
                 // MLST scheme:
-                params.mlst_scheme
-                    ? mlst_arg(params.mlst_scheme) : ""
+                params.mlst_scheme && (params.mlst_scheme != "None")
+                    ? mlst_arg(params.mlst_scheme) : "",
+
+                // Additional parameters
+                params.minimum_contig_length
+                    ? minimum_contig_length_arg(params.minimum_contig_length.toString()) : "",
+
+                params.genome_size_lower_bound
+                    ? genome_size_lower_bound_arg(params.genome_size_lower_bound.toString()) : "",
+
+                params.genome_size_upper_bound
+                    ? genome_size_upper_bound_arg(params.genome_size_upper_bound.toString()) : "",
+
+                params.minimum_N50_value
+                    ? minimum_N50_value_arg(params.minimum_N50_value.toString()) : "",
+
+                params.minimum_contig_length
+                    ? minimum_contig_length_arg(params.minimum_contig_length.toString()) : "",
+
+                params.unacceptable_number_contigs
+                    ? unacceptable_number_contigs_arg(params.unacceptable_number_contigs.toString()) : "",
+
+                params.pid_threshold
+                    ? pid_threshold_arg(params.pid_threshold.toString()) : "",
+
+                params.percent_length_overlap_plasmidfinder
+                    ? percent_length_overlap_plasmidfinder_arg(params.percent_length_overlap_plasmidfinder.toString()) : "",
+
+                params.percent_length_overlap_resfinder
+                    ? percent_length_overlap_resfinder_arg(params.percent_length_overlap_resfinder.toString()) : "",
+
+                params.percent_length_overlap_pointfinder
+                    ? percent_length_overlap_pointfinder_arg(params.percent_length_overlap_pointfinder.toString()) : "",
+
+                params.no_exclude_genes
+                    ? no_exclude_genes_arg : "",
+
+                params.exclude_negatives
+                    ? exclude_negatives_arg : "",
+
+                params.exclude_resistance_phenotypes
+                    ? exclude_resistance_phenotypes_arg : ""
             ].join(" ")
         }
     }

nextflow.config

@@ -50,10 +50,26 @@ params {
     validationShowHiddenParams       = false
     validate_params                  = true
 
-    //StarAMR options
-    pointfinder_database             = null
-    plasmidfinder_database           = null
-    mlst_scheme                      = null
+    // StarAMR options
+
+    // Databases
+    pointfinder_database             = "Automatic Selection"
+    plasmidfinder_database           = "All"
+    mlst_scheme                      = "None"
+
+    // Additional CLI arguments
+    genome_size_lower_bound              = 4000000
+    genome_size_upper_bound              = 6000000
+    minimum_N50_value                    = 10000
+    minimum_contig_length                = 300
+    unacceptable_number_contigs          = 1000
+    pid_threshold                        = 98
+    percent_length_overlap_plasmidfinder = 60
+    percent_length_overlap_resfinder     = 60
+    percent_length_overlap_pointfinder   = 95
+    no_exclude_genes                      = false
+    exclude_negatives                    = false
+    exclude_resistance_phenotypes        = false
 
 }
 

nextflow_schema.json

@@ -38,6 +38,119 @@
                 }
             }
         },
+        "database": {
+            "title": "Databases",
+            "type": "object",
+            "description": "Select databases to be run on all samples.",
+            "fa_icon": "fas fa-terminal",
+            "properties": {
+                "pointfinder_database": {
+                    "enum": [
+                        "Automatic Selection",
+                        "Enterococcus faecium",
+                        "Enterococcus faecalis",
+                        "Helicobacter pylori",
+                        "Salmonella",
+                        "Campylobacter",
+                        "Escherichia coli"
+                    ],
+                    "description": "Select a single Pointfinder database to use on all samples (overriding metadata option). Validated Organisms: Enterococcus faecium, Enterococcus faecalis, Helicobacter pylori, Salmonella, Campylobacter, Escherichia coli"
+                },
+                "plasmidfinder_database": {
+                    "enum": ["All", "gram_positive", "enterobacteriales"],
+                    "description": "The database type to use for plasmidfinder {gram_positive, enterobacteriales}. Defaults to using all available database types to search for plasmids. [All]."
+                },
+                "mlst_scheme": {
+                    "type": "string",
+                    "description": "Specify scheme name, visit https://github.com/tseemann/mlst/tree/master/db/pubmlst for supported scheme genera available. [None]",
+                    "default": "None"
+                }
+            }
+        },
+        "additional_settings": {
+            "title": "Additional Settings",
+            "type": "object",
+            "description": "For advanced changes to staramr",
+            "properties": {
+                "genome_size_lower_bound": {
+                    "type": "integer",
+                    "description": "The lower bound for our genome size for the quality metrics [Default 4000000]",
+                    "default": 4000000,
+                    "minimum": 1,
+                    "maximum" : 14000000
+                },
+                "genome_size_upper_bound": {
+                    "type": "integer",
+                    "description": "The upper bound for our genome size for the quality metrics [Default 6000000].",
+                    "default": 6000000,
+                    "minimum": 1,
+                    "maximum" : 14000000
+                },
+                "minimum_N50_value": {
+                    "type": "integer",
+                    "description": "The minimum N50 value for the quality metrics [Defaults 10000]",
+                    "default": 10000,
+                    "minimum": 1,
+                    "maximum" : 14000000
+
+                },
+                "minimum_contig_length": {
+                    "type": "integer",
+                    "description": "The minimum contig length for the quality metrics [Default 300 bp]",
+                    "default": 300,
+                    "minimum": 1,
+                    "maximum" : 14000000
+                },
+                "unacceptable_number_contigs": {
+                    "type": "integer",
+                    "description": "The minimum, unacceptable number of contigs which are equal to or above the minimum contig length for our quality metrics [Default 1000]",
+                    "default": 1000,
+                    "minimum": 1,
+                    "maximum" : 500000
+                },
+                "pid_threshold": {
+                    "type": "integer",
+                    "description": "BLAST percent identity threshold [Default 98]",
+                    "default": 98,
+                    "minimum": 1,
+                    "maximum" : 100
+                },
+                "percent_length_overlap_plasmidfinder": {
+                    "type": "integer",
+                    "description": "The percent length overlap for resfinder results [Default 60.0]",
+                    "default": 60,
+                    "minimum": 1,
+                    "maximum" : 100
+                },
+                "percent_length_overlap_resfinder": {
+                    "type": "integer",
+                    "description": "The percent length overlap for resfinder results [Default 60.0]",
+                    "default": 60,
+                    "minimum": 1,
+                    "maximum" : 100
+                },
+                "percent_length_overlap_pointfinder": {
+                    "type": "integer",
+                    "description": "The percent length overlap for pointfinder results [Default 95.0]",
+                    "default": 95,
+                    "minimum": 1,
+                    "maximum" : 100
+                },
+                "no_exclude_genes": {
+                    "type": "boolean",
+                    "description": "Disable the default exclusion of some genes from ResFinder/PointFinder/PlasmidFinder [Default False]"
+                },
+                "exclude_negatives": {
+                    "type": "boolean",
+                    "description": "Exclude negative results (those susceptible to antimicrobials) [DefaultFalse]"
+                },
+                "exclude_resistance_phenotypes": {
+                    "type": "boolean",
+                    "description": "Exclude predicted antimicrobial resistances [Default False]."
+                }
+            },
+            "fa_icon": "fas fa-terminal"
+        },
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -232,6 +345,12 @@
         {
             "$ref": "#/definitions/input_output_options"
         },
+        {
+            "$ref": "#/definitions/database"
+        },
+        {
+            "$ref": "#/definitions/additional_settings"
+        },
         {
             "$ref": "#/definitions/reference_genome_options"
         },
@@ -244,16 +363,5 @@
         {
             "$ref": "#/definitions/generic_options"
         }
-    ],
-    "properties": {
-        "pointfinder_database": {
-            "type": "string"
-        },
-        "plasmidfinder_database": {
-            "type": "string"
-        },
-        "mlst_scheme": {
-            "type": "string"
-        }
-    }
+    ]
 }

tests/main.nf.test

@@ -9,6 +9,7 @@ nextflow_pipeline {
             params {
                 input = "$baseDir/tests/assets/test_samplesheet.csv"
                 outdir = "$baseDir/tests/results"
+                max_memory = "4.GB"
             }
         }
 
@@ -51,6 +52,25 @@ nextflow_pipeline {
             assert ecoli_metadata."Scheme" == "ecoli_achtman_4"
             assert ecoli_metadata."Sequence Type" == "678"
 
+            // Check the commandline parameters
+            // Salmonella
+            assert path("$baseDir/tests/results/staramr/GCA_000008105_results/GCA_000008105_settings.txt").exists()
+            def salmonella_settings = new File("$baseDir/tests/results/staramr/GCA_000008105_results/GCA_000008105_settings.txt")
+            def salmonella_cmd = salmonella_settings.readLines().get(0)
+            assert salmonella_cmd == "command_line                  = /usr/local/bin/staramr search --pointfinder-organism salmonella --minimum-contig-length 300 --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000 --pid-threshold 98 --percent-length-overlap-plasmidfinder 60 --percent-length-overlap-resfinder 60 --percent-length-overlap-pointfinder 95 --nprocs 1 -o GCA_000008105_results GCA_000008105.fasta"
+
+            // Ecoli
+            assert path("$baseDir/tests/results/staramr/GCA_000947975_results/GCA_000947975_settings.txt").exists()
+            def ecoli_settings = new File("$baseDir/tests/results/staramr/GCA_000947975_results/GCA_000947975_settings.txt")
+            def ecoli_cmd = ecoli_settings.readLines().get(0)
+            assert ecoli_cmd == "command_line                  = /usr/local/bin/staramr search --pointfinder-organism escherichia_coli --minimum-contig-length 300 --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000 --pid-threshold 98 --percent-length-overlap-plasmidfinder 60 --percent-length-overlap-resfinder 60 --percent-length-overlap-pointfinder 95 --nprocs 1 -o GCA_000947975_results GCA_000947975.fasta"
+
+            // Listeria
+            assert path("$baseDir/tests/results/staramr/GCF_000196035_results/GCF_000196035_settings.txt").exists()
+            def listeria_settings = new File("$baseDir/tests/results/staramr/GCF_000196035_results/GCF_000196035_settings.txt")
+            def listeria_cmd = listeria_settings.readLines().get(0)
+            assert listeria_cmd == "command_line                  = /usr/local/bin/staramr search --minimum-contig-length 300 --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000 --pid-threshold 98 --percent-length-overlap-plasmidfinder 60 --percent-length-overlap-resfinder 60 --percent-length-overlap-pointfinder 95 --nprocs 1 -o GCF_000196035_results GCF_000196035.fasta"
+
             // Check CSVTK_concat output (merged_*) files
 
             // merged_detailed_summary.tsv