From 8b86406b42f2a1f464f473bc664825ea9e9a6c2b Mon Sep 17 00:00:00 2001
From: Jennifer Neumaier <jennifer.neumaier@tuta.com>
Date: Thu, 9 Apr 2026 13:18:05 +0200
Subject: [PATCH 1/2] fixed issue in 03_index that required a sorted bam file
 before indexing

---
 modules/02_star.nf  |  2 +-
 modules/03_index.nf | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/modules/02_star.nf b/modules/02_star.nf
index 2c2a3f0..cab7122 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -18,7 +18,7 @@ process STAR {
 
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
-    sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : ""
+    sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : "Unsorted"
     """
     STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
diff --git a/modules/03_index.nf b/modules/03_index.nf
index 7162aef..4ce15bf 100644
--- a/modules/03_index.nf
+++ b/modules/03_index.nf
@@ -16,9 +16,19 @@ process INDEX_BAM {
       file("software_versions.INDEX_BAM.txt")
 
     """
-    samtools index -@ ${task.cpus} ${bam}
+
+    samtools sort \
+    -@ ${task.cpus} \
+    -o ${name}.sorted.bam ${bam}
+
+    samtools index \
+    -@ ${task.cpus} ${name}.sorted.bam 
+
+    mv ${name}.sorted.bam.bai ${name}.bam.bai
+  
+    rm -f ${name}.sorted.bam
 
     echo ${params.manifest} >> software_versions.INDEX_BAM.txt
     samtools --version >> software_versions.INDEX_BAM.txt
     """
-}
+}
\ No newline at end of file

From 9f1fcd0557628f142f917903266f24f6771026e7 Mon Sep 17 00:00:00 2001
From: Jennifer Neumaier <jennifer.neumaier@tuta.com>
Date: Fri, 10 Apr 2026 14:44:01 +0200
Subject: [PATCH 2/2] added fix to handle automatic sorting of bam files were
 created by STAR alignment

---
 modules/02_star.nf  | 18 +++++++++++++++---
 modules/03_index.nf | 12 +-----------
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/modules/02_star.nf b/modules/02_star.nf
index cab7122..9c9b620 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -32,7 +32,13 @@ process STAR {
     --runThreadN ${task.cpus} \
     --outFileNamePrefix ${name}.
 
-    mv ${name}.Aligned*.out.bam ${name}.bam
+    # Handle sorting conditionally
+    if [ "${sort}" = "Unsorted" ]; then
+        samtools sort -@ ${task.cpus} -o ${name}.Aligned.SamtoolsSorted.out.bam ${name}.Aligned.out.bam
+        mv ${name}.Aligned.SamtoolsSorted.out.bam ${name}.bam
+    else
+        mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
+    fi
 
     echo ${params.manifest} >> software_versions.STAR.txt
     STAR --version >> software_versions.STAR.txt
@@ -58,7 +64,7 @@ process STAR_SE {
 
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
-    sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : ""
+    sort = params.star_sort_by_coordinate ? "SortedByCoordinate" : "Unsorted"
     """
     STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
@@ -72,7 +78,13 @@ process STAR_SE {
     --runThreadN ${task.cpus} \
     --outFileNamePrefix ${name}.
 
-    mv ${name}.Aligned*.out.bam ${name}.bam
+    # Handle sorting conditionally
+    if [ "${sort}" = "Unsorted" ]; then
+        samtools sort -@ ${task.cpus} -o ${name}.Aligned.SamtoolsSorted.out.bam ${name}.Aligned.out.bam
+        mv ${name}.Aligned.SamtoolsSorted.out.bam ${name}.bam
+    else
+        mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
+    fi
 
     echo ${params.manifest} >> software_versions.STAR_SE.txt
     STAR --version >> software_versions.STAR_SE.txt
diff --git a/modules/03_index.nf b/modules/03_index.nf
index 4ce15bf..1ba4df6 100644
--- a/modules/03_index.nf
+++ b/modules/03_index.nf
@@ -16,17 +16,7 @@ process INDEX_BAM {
       file("software_versions.INDEX_BAM.txt")
 
     """
-
-    samtools sort \
-    -@ ${task.cpus} \
-    -o ${name}.sorted.bam ${bam}
-
-    samtools index \
-    -@ ${task.cpus} ${name}.sorted.bam 
-
-    mv ${name}.sorted.bam.bai ${name}.bam.bai
-  
-    rm -f ${name}.sorted.bam
+    samtools index -@ ${task.cpus} ${bam}
 
     echo ${params.manifest} >> software_versions.INDEX_BAM.txt
     samtools --version >> software_versions.INDEX_BAM.txt