Make the AdapterSS2 wdl accept optional output, e.g. the zarr output. (#115)

* Make the AdapterSS2 wdl accept optional output, e.g. the zarr output.

* Prepare the release by updating the pipeline_tools_version.

Author: rexwangcc

adapter_pipelines/Optimus/adapter.wdl

@@ -127,7 +127,7 @@ workflow AdapterOptimus {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.43.1"
+  String pipeline_tools_version = "v0.44.0"
 
   call GetInputs as prep {
     input:

adapter_pipelines/cellranger/adapter.wdl

@@ -151,7 +151,7 @@ workflow Adapter10xCount {
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.43.1"
+  String pipeline_tools_version = "v0.44.0"
 
   call GetInputs {
     input:

adapter_pipelines/ss2_single_sample/adapter.wdl

@@ -83,7 +83,7 @@ workflow AdapterSmartSeq2SingleCell{
   Int max_cromwell_retries = 0
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.43.1"
+  String pipeline_tools_version = "v0.44.0"
 
   call GetInputs as prep {
     input:
@@ -177,18 +177,21 @@ workflow AdapterSmartSeq2SingleCell{
           "value": stranded
         }
       ],
-      outputs = flatten([[
-        analysis.aligned_bam,
-        analysis.bam_index,
-        analysis.insert_size_metrics,
-        analysis.quality_distribution_metrics,
-        analysis.quality_by_cycle_metrics,
-        analysis.bait_bias_summary_metrics,
-        analysis.rna_metrics,
-        analysis.aligned_transcriptome_bam,
-        analysis.rsem_gene_results,
-        analysis.rsem_isoform_results
-      ], analysis.group_results, analysis.zarr_output_files]),
+      outputs = flatten(
+        select_all(
+          [[analysis.aligned_bam,
+            analysis.bam_index,
+            analysis.insert_size_metrics,
+            analysis.quality_distribution_metrics,
+            analysis.quality_by_cycle_metrics,
+            analysis.bait_bias_summary_metrics,
+            analysis.rna_metrics,
+            analysis.aligned_transcriptome_bam,
+            analysis.rsem_gene_results,
+            analysis.rsem_isoform_results
+           ], analysis.group_results, analysis.zarr_output_files]
+        )
+      ),
       format_map = format_map,
       submit_url = submit_url,
       cromwell_url = cromwell_url,