Merge pull request #23 from msk-access/main

main->develop
msk-access · Aug 8, 2023 · 6477880 · 6477880
2 parents dc4b5ca + 7c550ca
commit 6477880
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Showing 6 changed files with 105 additions and 111 deletions.
diff --git a/cwl-commandlinetools b/cwl-commandlinetools
diff --git a/cwl_subworkflows b/cwl_subworkflows
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