Merge pull request #7 from eastgenomics/dev

Make chimeric junction file output optional (#7)
eastgenomics · Jun 17, 2024 · 1a1eb40 · 1a1eb40
2 parents 073d9dc + 46781eb
commit 1a1eb40
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/src/script.sh b/src/script.sh
@@ -206,10 +206,13 @@ sentieon util index /home/dnanexus/out/${sample_name}.mark_duplicates.star.Proce
 # Move output files to /out directory so they will be uploaded
 mv /home/dnanexus/out/${sample_name}.star.bam /home/dnanexus/out/output_bam
 mv /home/dnanexus/out/${sample_name}.star.bam.bai /home/dnanexus/out/output_bam_bai
-mv /home/dnanexus/Chimeric.out.junction /home/dnanexus/out/chimeric_junctions/${sample_name}.chimeric.out.junction
 mv /home/dnanexus/out/${sample_name}.mark_duplicates.star.Processed.out.bam /home/dnanexus/out/output_mark_duplicates_bam
 mv /home/dnanexus/out/${sample_name}.mark_duplicates.star.Processed.out.bam.bai /home/dnanexus/out/output_mark_duplicates_bam_bai
 for f in Log*; do mv "$f" "${sample_name}.$f"; done
 mv /home/dnanexus/${sample_name}.Log* /home/dnanexus/out/logs
 
+if [ -f *.chimeric.out.junction ]; then
+ mv /home/dnanexus/Chimeric.out.junction /home/dnanexus/out/chimeric_junctions/${sample_name}.chimeric.out.junction
+fi
+
 dx-upload-all-outputs