Merge pull request #1049 from MatthiasZepper/ExtraStarAlignArgsWarning

Display a warning when '--star_extra_alignment_args' are used with RSEM

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v3.13.0dev - [date]
+
+### Enhancements & fixes
+
+- [PR #1049](https://github.com/nf-core/rnaseq/pull/1049) - RSEM imposes own arguments to STAR, therefore `--extra_star_align_args` are ignored for this route. A warning is displayed when both are used together.
+
 ## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02
 
 ### Credits

lib/WorkflowRnaseq.groovy

@@ -86,6 +86,9 @@ class WorkflowRnaseq {
             if (params.rsem_index && params.star_index) {
                 rsemStarIndexWarn(log)
             }
+            if (params.aligner  == 'star_rsem' && params.extra_star_align_args) {
+                rsemStarExtraArgumentsWarn(log)
+            }
         }
 
         // Warn if --additional_fasta provided with aligner index
@@ -394,6 +397,19 @@ class WorkflowRnaseq {
             "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
     }
 
+    //
+    // Print a warning if using '--aligner star_rsem' and providing '--star_extra_alignment_args'
+    //
+    private static void rsemStarExtraArgumentsWarn(log) {
+        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
+            "  No additional arguments can be passed to STAR when using RSEM.\n" +
+            "  Because RSEM enforces its own parameters for STAR, any extra arguments\n" +
+            "  to STAR will be ignored. Alternatively, choose the STAR+Salmon route.\n\n" +
+            "  This warning has been generated because you have provided both\n" +
+            "  '--aligner star_rsem' and '--extra_star_align_args'.\n\n" +
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    }
+
     //
     // Print a warning if using '--additional_fasta' and '--<ALIGNER>_index'
     //

nextflow_schema.json

@@ -417,7 +417,7 @@
                 },
                 "extra_star_align_args": {
                     "type": "string",
-                    "description": "Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline.",
+                    "description": "Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline. Only available for the STAR-Salmon route.",
                     "fa_icon": "fas fa-plus"
                 },
                 "extra_salmon_quant_args": {