From b33a19dc70e3c41a68e5d5bbfdc9cdef83cbaaa6 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 20 Feb 2026 15:25:52 -0500
Subject: [PATCH 1/3] fix: remove STAR protrude params

fixes #260
---
 CHANGELOG.md                  | 2 ++
 workflow/rules/paired-end.smk | 4 ----
 workflow/rules/single-end.smk | 2 --
 3 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f61dbd2..ad923b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,7 @@
 ## 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.
+
 ## RENEE 2.7.4
 
 - New `--partition` option for `renee run` and `renee build` to specify the SLURM partition. (#252, @kelly-sovacool)
diff --git a/workflow/rules/paired-end.smk b/workflow/rules/paired-end.smk
index 5b39305..0cfe26f 100644
--- a/workflow/rules/paired-end.smk
+++ b/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}}
 
diff --git a/workflow/rules/single-end.smk b/workflow/rules/single-end.smk
index 8b9b39f..fa4bf55 100644
--- a/workflow/rules/single-end.smk
+++ b/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}}
 

From 01529d2f40b47512cf192b27f1533a23920231b2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 20 Feb 2026 15:29:54 -0500
Subject: [PATCH 2/3] chore: update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ad923b9..0a8f93b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +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.
+- 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)
 
 ## RENEE 2.7.4
 

From 9dfec6cb45018b1b1925f90afee0974378c5cd93 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 13 Mar 2026 15:57:36 +0000
Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/copilot-instructions.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index ab79ac9..d54d055 100644
--- a/.github/copilot-instructions.md
+++ b/.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"
+    }
 }
 ```