Allow user-defined panels

nf-core · Mar 19, 2024 · 29ddb75 · 29ddb75
1 parent 9285ccc
commit 29ddb75
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Showing 4 changed files with 27 additions and 25 deletions.
diff --git a/lib/Constants.groovy b/lib/Constants.groovy
@@ -8,7 +8,7 @@ class Constants {
     static List GENOMES_SUPPORTED  = ['GRCh37_hmf', 'GRCh38_hmf']
     static List GENOMES_DEFINED    = Constants.GENOMES_VERSION_37 + Constants.GENOMES_VERSION_38
 
-    static List PANELS_DEFINED     = ['tso500']
+    static List PANELS_SUPPORTED   = ['tso500']
 
 
     static String HMF_DATA_37_PATH = 'https://pub-29f2e5b2b7384811bdbbcba44f8b5083.r2.dev/hmf_reference_data/hmftools/5.34_37--2.tar.gz'

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -264,7 +264,7 @@ class Utils {
             }
 
             // Apply some required restrictions to targeted mode
-            if (run_config.mode === Constants.RunMode.TARGETED) {
+            if (run_config.mode === Constants.RunMode.TARGETED && !run_config.force_panel) {
 
                 // Do not allow normal DNA
                 if (Utils.hasNormalDna(meta)) {
@@ -281,13 +281,6 @@ class Utils {
                     System.exit(1)
                 }
 
-                // Restrict tumor RNA inputs to the TSO500 panel
-                if (Utils.hasTumorRnaBam(meta) && run_config.panel != 'tso500') {
-                    def panel = run_config.panel.toUpperCase()
-                        "Only the TSO500 panel supports tumor RNA analysis"
-                    System.exit(1)
-                }
-
             }
 
             // Do not allow normal DNA only

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -276,24 +276,27 @@ class WorkflowMain {
         if (run_mode === Constants.RunMode.TARGETED) {
 
             if (!params.containsKey('panel')) {
-
-                def panels = Constants.PANELS_DEFINED.join('\n    - ')
-                log.error "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                    "  A panel is required to be set using the --panel CLI argument or in a \n" +
-                    "  configuration file.\n" +
-                    "  Currently, the available panels are:\n" +
-                    "    - ${panels}\n" +
-                    "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+                log.error "\n  A panel is required to be set using the --panel CLI argument or in configuration " +
+                    "file.\n  Currently, the available panels are:\n" +
+                    "    - ${Constants.PANELS_SUPPORTED.join('\n    - ')}"
                 System.exit(1)
 
-            } else if (!Constants.PANELS_DEFINED.contains(params.panel)) {
+            } else if (!Constants.PANELS_SUPPORTED.contains(params.panel)) {
+                if (params.containsKey('force_panel') && !params.force_panel) {
+                    log.error "\n  The ${params.panel} panel is not supported but you can force run the analysis using " +
+                        "this panel by setting --force_panel.\n  Currently, the supported panels are:\n" +
+                        "    - ${Constants.PANELS_SUPPORTED.join('\n    - ')}"
+                    System.exit(1)
+                } else {
+                    log.warn "got unsupported ${params.panel} panel but forcing to proceed"
+                }
 
-                def panels = Constants.PANELS_DEFINED.join('\n    - ')
-                log.error "\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-                    "  The ${params.panel} is not defined. Currently, the available panels are:\n" +
-                    "    - ${panels}\n" +
-                    "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-                System.exit(1)
+                if (!params.panel_data_paths.containsKey(params.panel)) {
+                    log.error "\n  The ${params.panel} panel is used but no filepaths were set in " +
+                        "params.panel_data_paths.\n  Currently, panels with defined filepaths are:\n" +
+                        "    - ${params.panel_data_paths.keySet().join('\n    - ')}"
+                    System.exit(1)
+                }
 
             }
 
@@ -315,6 +318,7 @@ class WorkflowMain {
         return [
             mode: run_mode,
             panel: run_mode === Constants.RunMode.TARGETED ? params.panel : null,
+            force_panel: params.containsKey('force_panel') ? params.force_panel : false,
             stages: stages,
             has_dna: inputs.any { Utils.hasTumorDna(it) },
             has_rna: inputs.any { Utils.hasTumorRna(it) },

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -58,7 +58,12 @@
                 },
                 "force_genome": {
                     "type": "boolean",
-                    "description": "Skip check for restricted genome.",
+                    "description": "Force use of unsupported genome.",
+                    "fa_icon": "fas fa-palette"
+                },
+                "force_panel": {
+                    "type": "boolean",
+                    "description": "Force use of unsupported panel.",
                     "fa_icon": "fas fa-palette"
                 },
                 "processes_manual": {