Allow panels to use tumor RNA input, minor fixes

nf-core · Sep 10, 2024 · d1e5f11 · d1e5f11
1 parent f81869e
commit d1e5f11
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Showing 2 changed files with 10 additions and 12 deletions.
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -278,25 +278,18 @@ class Utils {
                 }
 
                 // Do not allow only tumor RNA
-                if (Utils.hasTumorRnaBam(meta) && !Utils.hasTumorDna(meta)) {
+                if (Utils.hasTumorRna(meta) && !Utils.hasTumorDna(meta)) {
                     log.error "targeted mode is not compatible with only tumor RNA provided for ${meta.group_id}\n\n" +
                         "The targeted workflow requires tumor DNA and can optionally take tumor RNA, depending on " +
                         "the configured panel."
                     Nextflow.exit(1)
                 }
 
-                // Restrict tumor RNA inputs to the TSO500 panel
-                if (Utils.hasTumorRnaBam(meta) && run_config.panel != 'tso500') {
-                    def panel = run_config.panel.toUpperCase()
-                    log.error "only the TSO500 panel supports tumor RNA analysis but got: ${panel}"
-                    Nextflow.exit(1)
-                }
-
             }
 
             // Do not allow normal DNA only
             if (Utils.hasNormalDna(meta) && !Utils.hasTumorDna(meta)) {
-                log.error "germline only mode not supported, found only a normal DNA BAM for ${meta.group_id}"
+                log.error "found only normal DNA input for ${meta.group_id} but germline only analysis is not supported"
                 Nextflow.exit(1)
             }
 

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -191,14 +191,19 @@ class WorkflowMain {
 
             } else if (!Constants.PANELS_DEFINED.contains(params.panel)) {
 
-                if (!params.containsKey('force_panel') && !params.force_panel) {
+                if (params.containsKey('force_panel') && params.force_panel) {
+                    log.warn "provided panel ${params.panel} does not have built-in support but forcing to proceed"
+                } else {
                     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" +
+                        "  The ${params.panel} panel does not have built-in support. Currently, the\n" +
+                        "  available supported panels are:\n" +
+                        "    - ${panels}\n\n" +
+                        "  Please adjust the --panel argument or override with --force_panel.\n" +
                         "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
                     Nextflow.exit(1)
                 }
+
             }
         }