Merge pull request broadinstitute#449 from broadinstitute/gg_GL-1736_…

…DoNotWriteFingerprintsToMercuryForControlSamples

GL-1736. Don't write control fingerprints to the Mercury Fingerprint Store

pipelines/broad/arrays/single_sample/Arrays.changelog.md

@@ -1,7 +1,8 @@
 # 2.4.3
-2021-09-24
+2021-09-27
 
 * Enabled pipeline to lookup the cluster_file using an alternate method (using the arrays_metadata_path and cluster_filename)
+* Modified pipeline to NOT write fingerprints for control samples to the Mercury Fingerprint Store.
 
 # 2.4.2
 2021-09-22

pipelines/broad/arrays/single_sample/Arrays.wdl

@@ -183,8 +183,8 @@ workflow Arrays {
     }
   }
 
-  String bpm_filename = if (defined(bead_pool_manifest_file)) then select_first([bead_pool_manifest_file]) else select_first([bead_pool_manifest_filename, ""])
-  String chip_type = basename(bpm_filename, ".bpm")
+  String bpm_filename = if (defined(bead_pool_manifest_file)) then basename(select_first([bead_pool_manifest_file])) else select_first([bead_pool_manifest_filename, ""])
+  String chip_type = sub(bpm_filename, ".bpm", "")
   File bpm_file = if (defined(bead_pool_manifest_file)) then select_first([bead_pool_manifest_file]) else select_first([arrays_metadata_path, ""]) + chip_type + "/" + select_first([bead_pool_manifest_filename, ""])
 
   if (!defined(cluster_filename) && !defined(cluster_file)) {
@@ -378,7 +378,8 @@ workflow Arrays {
         preemptible_tries = preemptible_tries
     }
 
-    if (write_fingerprint_to_mercury) {
+    # Only write fingerprints to the Mercury Fingerprint Store if writing is enabled AND the sample is NOT a control
+    if (write_fingerprint_to_mercury && (!defined(control_sample_name))) {
       call InternalTasks.UploadFingerprintToMercury {
         input:
           fingerprint_json_file = VcfToMercuryFingerprintJson.output_json_file,