Fix samtools sorting error in demo pipeline
@@ -73,7 +73,7 @@ do
SORTED_OUTPUT=$SAMPLE_NAME_CURRENT/3_sort
mkdir -p $SORTED_OUTPUT
pipe_log_info "Started BAM sort and index" "$SAMPLE_NAME_CURRENT"
- $SAMTOOLS_BIN sort -f $BWA_OUTPUT/$SAMPLE_NAME_CURRENT.unsorted.bam $SORTED_OUTPUT/$SAMPLE_NAME_CURRENT.sorted.bam
+ $SAMTOOLS_BIN sort -@ $(nproc) $BWA_OUTPUT/$SAMPLE_NAME_CURRENT.unsorted.bam $SORTED_OUTPUT/$SAMPLE_NAME_CURRENT.sorted
$SAMTOOLS_BIN index $SORTED_OUTPUT/$SAMPLE_NAME_CURRENT.sorted.bam
finish_task $SAMPLE_NAME_CURRENT $?
