Merge pull request #681 from drpatelh/updates

FIx #556

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * Updated pipeline template to [nf-core/tools 2.1](https://github.com/nf-core/tools/releases/tag/2.1)
+* [[#556](https://github.com/nf-core/rnaseq/issues/556)] - Genome index isn't recreated with --additional_fasta unless --star_index false
 * [[#668](https://github.com/nf-core/rnaseq/issues/668)] - Salmon quant with UMI-tools does not work
 * [[#674](https://github.com/nf-core/rnaseq/issues/674)] - Launch pipeline regex fails
 

lib/WorkflowRnaseq.groovy

@@ -67,6 +67,23 @@ class WorkflowRnaseq {
             }
         }
 
+        // Warn if --additional_fasta provided with aligner index
+        if (!params.skip_alignment && params.additional_fasta) {
+            def index = ''
+            if (params.aligner == 'star_salmon' && params.star_index) {
+                index = 'star'
+            }
+            if (params.aligner == 'star_rsem' && params.rsem_index) {
+                index = 'rsem'
+            }
+            if (params.aligner == 'hisat2' && params.hisat2_index) {
+                index = 'hisat2'
+            }
+            if (index) {
+                additionaFastaIndexWarn(index, log)
+            }
+        }
+
         // Check which RSeQC modules we are running
         def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
         if ((valid_params['rseqc_modules'] + rseqc_modules).unique().size() != valid_params['rseqc_modules'].size()) {
@@ -260,4 +277,21 @@ class WorkflowRnaseq {
             "  https://github.com/nf-core/rnaseq/issues/568\n" +
             "==================================================================================="
     }
+
+    //
+    // Print a warning if using '--additional_fasta' and '--<ALIGNER>_index'
+    //
+    private static void additionaFastaIndexWarn(index, log) {
+        log.warn "=============================================================================\n" +
+            "  When using '--additional_fasta <FASTA_FILE>' the aligner index will not\n" +
+            "  be re-built with the transgenes incorporated by default since you have \n" +
+            "  already provided an index via '--${index}_index <INDEX>'.\n\n" +
+            "  Set '--additional_fasta <FASTA_FILE> --${index}_index false --save_reference' to\n" +
+            "  re-build the index with transgenes included and the index will be saved in\n" +
+            "  'results/genome/index/${index}/' for re-use with '--${index}_index'.\n\n" +
+            "  Ignore this warning if you know that the index already contains transgenes.\n\n" +
+            "  Please see:\n" +
+            "  https://github.com/nf-core/rnaseq/issues/556\n" +
+            "==================================================================================="
+    }
 }