updating working version

carmelinacharalambous · carmelinacharalambous · commit 19c8d9911f83 · 2023-08-08T12:46:30.000-04:00
diff --git a/cwl-commandlinetools b/cwl-commandlinetools
@@ -1 +1 @@
-Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133
+Subproject commit 8974f3c04d284656f13671a721c8717583d5f756
diff --git a/cwl_subworkflows b/cwl_subworkflows
@@ -1 +1 @@
-Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88
+Subproject commit c40a06349a395024b68fc11ff9acd3433491fe4f
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_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
