Merge branch 'release/1.1.3'

Author: rhshah

generate_aggregate.cwl

@@ -26,6 +26,10 @@ inputs:
     type: File
     'sbg:x': 0
     'sbg:y': 1813.921875
+  - id: biometrics_bed_file
+    type: File
+    'sbg:x': 0
+    'sbg:y': 1813.921875
   - id: collapsed_bam
     type: 'File[]'
     'sbg:x': 0
@@ -146,13 +150,6 @@ outputs:
     type: Directory
     'sbg:x': 1585.9033203125
     'sbg:y': 1440.421875
-  - id: pickle_files_dir
-    outputSource:
-      - pickle_files/directory
-    type: Directory
-    label: pickle_files_dir
-    'sbg:x': 1582
-    'sbg:y': 993
 steps:
   - id: qc_generator
     in:
@@ -182,6 +179,8 @@ steps:
         source: simplex_bam
       - id: vcf_file
         source: biometrics_vcf_file
+      - id: biometrics_bed_file
+        source: biometrics_bed_file
       - id: hotspots_maf
         source: hotspots_maf
       - id: mosdepth_bed
@@ -286,21 +285,6 @@ steps:
     label: qc_aggregator
     'sbg:x': 1076.5557861328125
     'sbg:y': 1270.734375
-  - id: pickle_files
-    in:
-      - id: files
-        linkMerge: merge_flattened
-        source:
-          - qc_generator/collapsed_biometrics_extract_pickle
-          - qc_generator/duplex_biometrics_extract_pickle
-      - id: output_directory_name
-        default: pickle_files
-    out:
-      - id: directory
-    run: cwl-commandlinetools/expression_tools/put_in_dir.cwl
-    label: pickle_files
-    'sbg:x': 1283.092529296875
-    'sbg:y': 981.6953125
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement

nucleo_qc.cwl

@@ -28,6 +28,10 @@ inputs:
     type: File
     'sbg:x': 0
     'sbg:y': 2030.03125
+  - id: biometrics_bed_file
+    type: File
+    'sbg:x': 0
+    'sbg:y': 2030.03125
   - id: collapsed_bam
     type: 'File[]'
     'sbg:x': 0
@@ -197,6 +201,8 @@ steps:
         source: simplex_bam
       - id: vcf_file
         source: biometrics_vcf_file
+      - id: biometrics_bed_file
+        source: biometrics_bed_file
       - id: hotspots_maf
         source: hotspots_maf
       - id: mosdepth_bed

qc_generator/nucleo_qc_generator.cwl

@@ -95,6 +95,10 @@ inputs:
     doc: Also output data in JSON format.
     'sbg:x': 0
     'sbg:y': 2777.53125
+  - id: biometrics_bed_file
+    type: File?
+    'sbg:x': -423.2972106933594
+    'sbg:y': 2095.491455078125
   - id: collapsed_biometrics_minor_threshold
     type: float?
     label: collapsed_biometrics_minor_threshold
@@ -145,8 +149,8 @@ inputs:
     'sbg:y': 1922.90625
   - id: mosdepth_bed
     type: File?
-    'sbg:x': 0
-    'sbg:y': 1495.59375
+    'sbg:x': -359.3104248046875
+    'sbg:y': 1495
   - id: mosdepth_flag
     type: int?
     'sbg:x': 0
@@ -200,8 +204,12 @@ inputs:
     type: boolean?
   - id: fragment_count
     type: int
+    'sbg:x': 300.2456970214844
+    'sbg:y': 0
   - id: filter_duplicate
     type: int
+    'sbg:x': 170.50595092773438
+    'sbg:y': -103.53236389160156
 outputs:
   - id: uncollapsed_bam_stats_dir
     outputSource:
@@ -309,6 +317,8 @@ steps:
         source: biometrics_json
       - id: plot
         source: biometrics_plot
+      - id: bed_file
+        source: biometrics_bed_file
       - id: minor_threshold
         source: collapsed_biometrics_minor_threshold
       - id: coverage_threshold
@@ -519,8 +529,8 @@ steps:
       - id: coverage_report_single
     run: ../cwl_subworkflows/athena_report/athena_report.cwl
     label: athena_report
-    'sbg:x': 1378
-    'sbg:y': 2784
+    'sbg:x': 1382.922119140625
+    'sbg:y': 2798.76611328125
   - id: simplex_bam_stats
     in:
       - id: files

requirements.txt

@@ -1,7 +1,6 @@
 coloredlogs==15.0.1
 pytest==7.2.0
 setuptools==65.4.1
-cwltool==3.1.20230425144158
-toil[cwl] @ git+https://github.com/DataBiosphere/toil.git
+toil[cwl]==5.10.0
 pytest-runner==6.0.0
 tox==3.27.1