update nextflow options

main.nf

@@ -15,9 +15,33 @@ process run_piranha {
         path "published_data"
 
     script:
+    extra = ""
+    if ( params.config )
+        extra += " --config ${params.config}"
+    if ( params.output_intermediates )
+        extra += " --no-temp"
+    if ( params.min_map_quality )
+        extra += " --min-map-quality ${params.min_map_quality}"
+    if ( params.min_read_length )
+        extra += " --min-read-length ${params.min_read_length}"
+    if ( params.max_read_length )
+        extra += " --max-read-length ${params.max_read_length}"
+    if ( params.min_read_depth )
+        extra += " --min-read-depth ${params.min_read_depth}"
+    if ( params.min_read_pcent )
+        extra += " --min-read-pcent ${params.min_read_pcent}"
+    if ( params.primer_length )
+        extra += " --primer-length ${params.primer_length}"
+    if ( params.run_phylo )
+        extra += " --run-phylo"
+    if ( params.supplementary_sequences )
+        extra += " --supplementary-sequences ${params.supplementary_sequences}"
+     if ( params.supplementary_metadata )
+            extra += " --supplementary-metadata ${params.supplementary_metadata}"
     """
-    piranha -b ${barcodes_csv} -i ${run_dir} -o piranha_output --tempdir piranha_tmp -t ${task.cpus}
+    piranha -b ${barcodes_csv} -i ${run_dir} -o piranha_output --tempdir piranha_tmp -t ${task.cpus} ${extra}
     mv piranha_output/* .
+    rm -rf piranha_output
     mv report.html piranha_report.html
     """
 

nextflow.config

@@ -18,6 +18,22 @@ params {
     run_dir = null
 
     out_dir = "output"
+    output_intermediates = false
+    config = null
+
+    // Analysis options
+    min_map_quality = null
+    min_read_length = null
+    max_read_length = null
+    min_read_depth = null
+    min_read_pcent = null
+    min_aln_block = null
+    primer_length = null
+
+    // Phylo options
+    run_phylo = false
+    supplementary_sequences = null
+    supplementary_metadata = null
 
     // Other options
     disable_ping = false

nextflow_schema.json

@@ -42,24 +42,81 @@
     "output_options": {
       "title": "Output Options",
       "type": "object",
+      "fa_icon": "fas fa-terminal",
       "description": "Parameters for saving and naming workflow outputs.",
-      "default": "",
       "properties": {
         "out_dir": {
           "type": "string",
           "format": "directory-path",
           "default": "output",
           "title": "Output folder name",
           "description": "Directory for output of all user-facing files."
+        },
+        "output_intermediates": {
+          "type": "boolean",
+          "title": "Output intermediate files"
         }
       }
     },
-    "advanced_options": {
-      "title": "Advanced Options",
+    "analysis_options": {
+      "title": "Analysis Options",
       "type": "object",
-      "description": "Advanced options for configuring processes inside the workflow.",
-      "default": "",
+      "fa_icon": "fas fa-terminal",
+      "description": "Define the thresholds for filtering and assembly.",
       "properties": {
+        "config": {
+          "type": "string",
+          "format": "path",
+          "title": "Config file",
+          "description": "A config file with parameters for piranha."
+        },
+        "min_map_quality": {
+          "type": "integer",
+          "title": "Minimum mapping quality"
+        },
+        "min_read_length": {
+          "type": "integer",
+          "title": "Minimum read length"
+        },
+        "max_read_length": {
+          "type": "integer",
+          "title": "Maximum read length"
+        },
+        "min_read_depth": {
+          "type": "integer",
+          "title": "Minimum read depth required for consensus generation"
+        },
+        "min_read_pcent": {
+          "type": "number",
+          "title": "Minimum percentage of sample required for consensus generation"
+        },
+        "primer_length": {
+          "type": "integer",
+          "title": "Length of primer sequences to trim off start and end of reads"
+        }
+      }
+    },
+    "phylo_options": {
+      "title": "Phylogenetic Options",
+      "type": "object",
+      "description": "Options for running the phylogenetics module.",
+      "properties": {
+        "run_phylo": {
+          "type": "boolean",
+          "title": "Run phylogenetics pipeline"
+        },
+        "supplementary_sequences": {
+          "type": "string",
+          "format": "path",
+          "title": "Supplementary sequences",
+          "description": "Supplementary sequence FASTA file to be incorporated into phylogenetic analysis"
+        },
+        "supplementary_metadata": {
+          "type": "string",
+          "format": "path",
+          "title": "Supplementary metadata",
+          "description": " Supplementary metadata file associated with the supplementary sequence FASTA file"
+        }
       }
     },
     "miscellaneous_options": {
@@ -93,7 +150,10 @@
       "$ref": "#/definitions/output_options"
     },
     {
-      "$ref": "#/definitions/advanced_options"
+      "$ref": "#/definitions/analysis_options"
+    },
+    {
+      "$ref": "#/definitions/phylo_options"
     },
     {
       "$ref": "#/definitions/miscellaneous_options"