Debugging

Author: egreenberg7

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

@@ -274,7 +274,7 @@ def validateInputParameters() {
             brackenPrecisionWithoutKrakenDBWarn()
         }
 
-        if (params.save_kraken_assignments || params.save_kraken_unassigned) {
+        if (params.save_kraken_assignments || params.save_kraken_unassigned || params.kraken_db) {
             krakenArgumentsWithoutKrakenDBWarn()
         }
     }
@@ -499,9 +499,8 @@ def additionaFastaIndexWarn(index) {
 //
 def krakenArgumentsWithoutKrakenDBWarn() {
     log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-        "  '--save_kraken_assignments' or '--save_kraken_unassigned' parameters\n" +
-        "  have been provided when contaminant screening is not set to Kraken2.\n" +
-        "  Kraken2 is not being run so neither will be saved.\n" +
+        "  'Kraken2 related arguments have been provided without setting contaminant\n" +
+        "  screening to Kraken2. Kraken2 is not being run so these will not be used.\n" +
         "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
 }
 

workflows/rnaseq/main.nf

@@ -652,7 +652,7 @@ workflow RNASEQ {
 
             if (params.contaminant_screening == 'kraken2') {
                 ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.report.collect{it[1]})
-            } else if (params.contaminant_screening == 'kraken2_bracken')
+            } else if (params.contaminant_screening == 'kraken2_bracken') {
                 BRACKEN (
                     ch_kraken_reports,
                     params.kraken_db