Add thread limitation to samtools sort to avoid excessive memory request

sanger-pathogens · Jan 6, 2025 · bca6efc · bca6efc
1 parent 57b107c
commit bca6efc
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/bin/convert_sam_to_sorted_bam.sh b/bin/convert_sam_to_sorted_bam.sh
@@ -1,9 +1,13 @@
 # Convet SAM to sorted BAM file
 # Remove source SAM file if $LITE is true
 
-samtools view -@ "$(nproc)" -b "$SAM" > "$BAM"
+# Thread usage is capped as memory usage is per thread, and the speed gain level-off as thread count increases 
+AVAILABLE_THREAD=$(nproc)
+THREAD=$(( AVAILABLE_THREAD > MAX_THREAD ? MAX_THREAD : AVAILABLE_THREAD ))
 
-samtools sort -@ "$(nproc)" -o "$SORTED_BAM" "$BAM"
+samtools view -@ "$THREAD" -b "$SAM" > "$BAM"
+
+samtools sort -@ "$THREAD" -o "$SORTED_BAM" "$BAM"
 rm "$BAM"
 
 if [ "$LITE" = true ]; then

diff --git a/modules/mapping.nf b/modules/mapping.nf
@@ -67,11 +67,13 @@ process SAM_TO_SORTED_BAM {
 
     script:
     sorted_bam="${sample_id}_mapped_sorted.bam"
+    max_thread="8"
     """
     SAM="$sam"
     BAM="mapped.bam"
     SORTED_BAM="$sorted_bam"
     LITE="$lite"
+    MAX_THREAD="$max_thread"
 
     source convert_sam_to_sorted_bam.sh
     source get_ref_coverage.sh