Merge branch 'release/1.1.4'

rhshah · rhshah · commit 7c550ca4f7c4 · 2023-08-08T16:07:53.000-04:00
diff --git a/cwl-commandlinetools b/cwl-commandlinetools
@@ -1 +1 @@
-Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd
+Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133
diff --git a/cwl_subworkflows b/cwl_subworkflows
@@ -1 +1 @@
-Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7
+Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88
diff --git a/generate_aggregate.cwl b/generate_aggregate.cwl
@@ -207,6 +207,7 @@ steps:
       - id: output
         source: output
       - id: omaf
+        default: true
         source: omaf
       - id: generic_counting
         source: generic_counting
@@ -262,7 +263,7 @@ steps:
         source:
           - qc_generator/collapsed_bam_stats_dir
       - id: biometrics_extract_files_dir
-        source: 
+        source:
           - qc_generator/biometrics_extract_files_dir
       - id: collapsed_bam_duplex_metrics_dir
         source:
diff --git a/nucleo_aggregate_visualize.cwl b/nucleo_aggregate_visualize.cwl
@@ -178,7 +178,7 @@ steps:
         source: config
     out:
       - id: aggregate_parsed_stats
-    run: cwl-commandlinetools/cci_utils/0.3.0/general_stats_parse.cwl
+    run: cwl-commandlinetools/cci_utils/0.3.1/general_stats_parse.cwl
     label: general_stats_parse
     'sbg:x': 870.1131591796875
     'sbg:y': 520.0625
diff --git a/nucleo_qc.cwl b/nucleo_qc.cwl
@@ -230,6 +230,7 @@ steps:
       - id: output
         source: output
       - id: omaf
+        default: true
         source: omaf
       - id: generic_counting
         source: generic_counting
@@ -294,7 +295,7 @@ steps:
         source:
           - qc_generator/collapsed_bam_duplex_metrics_dir
       - id: biometrics_extract_files_dir
-        source: 
+        source:
           - qc_generator/biometrics_extract_files_dir
       - id: samples-json
         source: samples-json
diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl
@@ -340,6 +340,7 @@ steps:
       - id: maf
         source: hotspots_maf
       - id: omaf
+        default: true
         source: omaf
       - id: filter_duplicate
         default: 0
