fix: remove STAR protrude params

.github/copilot-instructions.md

@@ -148,17 +148,17 @@ Example:
 
 ```json
 {
-  "Insert CRAFT prompt": {
-    "prefix": "craft",
-    "body": [
-      "/* C: Context: Repo=${workspaceFolderBasename}; bioinformatics pipelines; NIH HPC (Biowulf/Helix); containers: quay.io/ccbr */",
-      "/* R: Rules: no PHI, no secrets, containerize, pin versions, follow style */",
-      "/* F: Flow: inputs/ -> results/, conf/, tests/ */",
-      "/* T: Tests: provide a one-line TEST_CMD and expected output */",
-      "",
-      "A: $1"
-    ],
-    "description": "Insert CRAFT prompt and place cursor at Actions"
-  }
+    "Insert CRAFT prompt": {
+        "prefix": "craft",
+        "body": [
+            "/* C: Context: Repo=${workspaceFolderBasename}; bioinformatics pipelines; NIH HPC (Biowulf/Helix); containers: quay.io/ccbr */",
+            "/* R: Rules: no PHI, no secrets, containerize, pin versions, follow style */",
+            "/* F: Flow: inputs/ -> results/, conf/, tests/ */",
+            "/* T: Tests: provide a one-line TEST_CMD and expected output */",
+            "",
+            "A: $1"
+        ],
+        "description": "Insert CRAFT prompt and place cursor at Actions"
+    }
 }
 ```

CHANGELOG.md

@@ -1,5 +1,6 @@
 ## RENEE development version
 
+- Fix RSEM failure with custom references containing short sequences (e.g., HPV-integrated genomes) by removing incompatible STAR alignment parameters (`--alignEndsProtrude` and `--peOverlapNbasesMin`), which caused reads to protrude beyond transcript boundaries. (#261, @kelly-sovacool)
 - Added more memory to rule `validator` (#263, @samarth8392)
 
 ## RENEE 2.7.4

workflow/rules/paired-end.smk

@@ -476,8 +476,6 @@ else:
             --runThreadN {threads} \
             --outFileNamePrefix {params.prefix}. \
             --outSAMtype BAM Unsorted \
-            --alignEndsProtrude 10 ConcordantPair \
-            --peOverlapNbasesMin 10 \
             --sjdbGTFfile {params.gtffile} \
             --outTmpDir=${{tmp}}/STARtmp_{wildcards.name} \
             --sjdbOverhang ${{readlength}}
@@ -604,8 +602,6 @@ else:
             --limitSjdbInsertNsj {params.nbjuncs} \
             --quantMode TranscriptomeSAM GeneCounts \
             --outSAMtype BAM Unsorted \
-            --alignEndsProtrude 10 ConcordantPair \
-            --peOverlapNbasesMin 10 \
             --outTmpDir=${{tmp}}/STARtmp_{wildcards.name} \
             --sjdbOverhang ${{readlength}}
 

workflow/rules/single-end.smk

@@ -319,8 +319,6 @@ if config['options']['star_2_pass_basic']:
             --limitSjdbInsertNsj {params.nbjuncs} \
             --quantMode TranscriptomeSAM GeneCounts \
             --outSAMtype BAM SortedByCoordinate \
-            --alignEndsProtrude 10 ConcordantPair \
-            --peOverlapNbasesMin 10 \
             --outTmpDir=${{tmp}}/STARtmp_{wildcards.name} \
             --sjdbOverhang ${{readlength}}