Merge branch 'release/1.2.1'

Author: rhshah

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master", "develop" ]
+  pull_request:
+    branches: [ "master" ]
+  schedule:
+    - cron: "50 22 * * 4"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

LICENSE

@@ -438,25 +438,25 @@ outputs:
     'sbg:y': 1175.28125
   - id: biometrics_major_plot
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_plot
+      - biometrics_major_0_2_14/biometrics_major_plot
     type: File?
     'sbg:x': 1547.1123046875
     'sbg:y': 1786.5
   - id: biometrics_major_json
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_json
+      - biometrics_major_0_2_14/biometrics_major_json
     type: File?
     'sbg:x': 1547.1123046875
     'sbg:y': 1893.34375
   - id: biometrics_major_csv
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_csv
+      - biometrics_major_0_2_14/biometrics_major_csv
     type: File
     'sbg:x': 1547.1123046875
     'sbg:y': 2000.1875
   - id: biometrics_extract_pickle
     outputSource:
-      - biometrics_extract_0_2_13/biometrics_extract_pickle
+      - biometrics_extract_0_2_14/biometrics_extract_pickle
     type: File
     'sbg:x': 982.1435546875
     'sbg:y': 3145.625
@@ -564,7 +564,7 @@ steps:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: minor_threshold
         source: minor_threshold
       - id: prefix
@@ -581,15 +581,15 @@ steps:
       - id: biometrics_minor_json
       - id: biometrics_minor_plot
       - id: biometrics_minor_sites_plot
-    run: ../command_line_tools/biometrics_minor/0.2.13/biometrics_minor.cwl
+    run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2847.9375
   - id: biometrics_sexmismatch
     in:
       - id: input
         linkMerge: merge_flattened
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: coverage_threshold
         source: coverage_threshold
       - id: prefix
@@ -601,15 +601,15 @@ steps:
       - id: biometrics_sexmismatch_csv
       - id: biometrics_sexmismatch_json
     run: >-
-      ../command_line_tools/biometrics_sexmismatch/0.2.13/biometrics_sexmismatch.cwl
+      ../command_line_tools/biometrics_sexmismatch/0.2.14/biometrics_sexmismatch.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2692.09375
-  - id: biometrics_major_0_2_13
+  - id: biometrics_major_0_2_14
     in:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: major_threshold
         source: major_threshold
       - id: prefix
@@ -622,10 +622,10 @@ steps:
       - id: biometrics_major_csv
       - id: biometrics_major_json
       - id: biometrics_major_plot
-    run: ../command_line_tools/biometrics_major/0.2.13/biometrics_major.cwl
+    run: ../command_line_tools/biometrics_major/0.2.14/biometrics_major.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 3010.78125
-  - id: biometrics_extract_0_2_13
+  - id: biometrics_extract_0_2_14
     in:
       - id: sample_bam
         source: collapsed_bam
@@ -643,7 +643,7 @@ steps:
         source: bed_file
     out:
       - id: biometrics_extract_pickle
-    run: ../command_line_tools/biometrics_extract/0.2.13/biometrics_extract.cwl
+    run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl
     'sbg:x': 351.4375
     'sbg:y': 1612.234375
   - id: getbasecountsmultisample_1_2_5

command_line_tools

@@ -321,25 +321,25 @@ outputs:
     'sbg:y': 884.875
   - id: biometrics_major_plot
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_plot
+      - biometrics_major_0_2_14/biometrics_major_plot
     type: File?
     'sbg:x': 1482.3623046875
     'sbg:y': 1496.25
   - id: biometrics_major_json
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_json
+      - biometrics_major_0_2_14/biometrics_major_json
     type: File?
     'sbg:x': 1482.3623046875
     'sbg:y': 1603.125
   - id: biometrics_major_csv
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_csv
+      - biometrics_major_0_2_14/biometrics_major_csv
     type: File
     'sbg:x': 1482.3623046875
     'sbg:y': 1710
   - id: biometrics_extract_pickle
     outputSource:
-      - biometrics_extract_0_2_13/biometrics_extract_pickle
+      - biometrics_extract_0_2_14/biometrics_extract_pickle
     type: File
     'sbg:x': 982.1435546875
     'sbg:y': 2214.5
@@ -401,7 +401,7 @@ steps:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: minor_threshold
         source: minor_threshold
       - id: prefix
@@ -418,15 +418,15 @@ steps:
       - id: biometrics_minor_json
       - id: biometrics_minor_plot
       - id: biometrics_minor_sites_plot
-    run: ../command_line_tools/biometrics_minor/0.2.13/biometrics_minor.cwl
+    run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 1916.75
   - id: biometrics_sexmismatch
     in:
       - id: input
         linkMerge: merge_flattened
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: coverage_threshold
         source: coverage_threshold
       - id: prefix
@@ -438,15 +438,15 @@ steps:
       - id: biometrics_sexmismatch_csv
       - id: biometrics_sexmismatch_json
     run: >-
-      ../command_line_tools/biometrics_sexmismatch/0.2.13/biometrics_sexmismatch.cwl
+      ../command_line_tools/biometrics_sexmismatch/0.2.14/biometrics_sexmismatch.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 1760.875
-  - id: biometrics_major_0_2_13
+  - id: biometrics_major_0_2_14
     in:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: major_threshold
         source: major_threshold
       - id: prefix
@@ -459,10 +459,10 @@ steps:
       - id: biometrics_major_csv
       - id: biometrics_major_json
       - id: biometrics_major_plot
-    run: ../command_line_tools/biometrics_major/0.2.13/biometrics_major.cwl
+    run: ../command_line_tools/biometrics_major/0.2.14/biometrics_major.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2079.625
-  - id: biometrics_extract_0_2_13
+  - id: biometrics_extract_0_2_14
     in:
       - id: sample_bam
         source: collapsed_bam
@@ -483,7 +483,7 @@ steps:
         source: collapsed_biometrics_extract_file_type
     out:
       - id: biometrics_extract_pickle
-    run: ../command_line_tools/biometrics_extract/0.2.13/biometrics_extract.cwl
+    run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl
     'sbg:x': 351.4375
     'sbg:y': 1328.9375
   - id: getbasecountsmultisample_1_2_5

qc_collapsed_bam/qc_collapsed_bam.cwl

@@ -306,49 +306,49 @@ outputs:
     'sbg:y': 427.375
   - id: biometrics_major_plot
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_plot
+      - biometrics_major_0_2_14/biometrics_major_plot
     type: File?
     'sbg:x': 1495.5341796875
     'sbg:y': 1331.125
   - id: biometrics_major_json
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_json
+      - biometrics_major_0_2_14/biometrics_major_json
     type: File?
     'sbg:x': 1495.5341796875
     'sbg:y': 1437.96875
   - id: biometrics_major_csv
     outputSource:
-      - biometrics_major_0_2_13/biometrics_major_csv
+      - biometrics_major_0_2_14/biometrics_major_csv
     type: File
     'sbg:x': 1495.5341796875
     'sbg:y': 1544.8125
   - id: biometrics_extract_pickle
     outputSource:
-      - biometrics_extract_0_2_13/biometrics_extract_pickle
+      - biometrics_extract_0_2_14/biometrics_extract_pickle
     type: File
     'sbg:x': 982.1435546875
     'sbg:y': 2448.5625
   - id: biometrics_minor_sites_plot
     outputSource:
-      - biometrics_minor_0_2_13/biometrics_minor_sites_plot
+      - biometrics_minor_0_2_14/biometrics_minor_sites_plot
     type: File?
     'sbg:x': 1495.5341796875
     'sbg:y': 903.75
   - id: biometrics_minor_plot
     outputSource:
-      - biometrics_minor_0_2_13/biometrics_minor_plot
+      - biometrics_minor_0_2_14/biometrics_minor_plot
     type: File?
     'sbg:x': 1495.5341796875
     'sbg:y': 1010.59375
   - id: biometrics_minor_json
     outputSource:
-      - biometrics_minor_0_2_13/biometrics_minor_json
+      - biometrics_minor_0_2_14/biometrics_minor_json
     type: File?
     'sbg:x': 1495.5341796875
     'sbg:y': 1117.4375
   - id: biometrics_minor_csv
     outputSource:
-      - biometrics_minor_0_2_13/biometrics_minor_csv
+      - biometrics_minor_0_2_14/biometrics_minor_csv
     type: File
     'sbg:x': 1495.5341796875
     'sbg:y': 1224.28125
@@ -444,12 +444,12 @@ steps:
     label: bam_qc_stats_pool_b
     'sbg:x': 351.4375
     'sbg:y': 1373.125
-  - id: biometrics_major_0_2_13
+  - id: biometrics_major_0_2_14
     in:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: major_threshold
         source: major_threshold
       - id: prefix
@@ -462,10 +462,10 @@ steps:
       - id: biometrics_major_csv
       - id: biometrics_major_json
       - id: biometrics_major_plot
-    run: ../command_line_tools/biometrics_major/0.2.13/biometrics_major.cwl
+    run: ../command_line_tools/biometrics_major/0.2.14/biometrics_major.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2313.71875
-  - id: biometrics_extract_0_2_13
+  - id: biometrics_extract_0_2_14
     in:
       - id: sample_bam
         source: duplex_bam
@@ -483,15 +483,15 @@ steps:
         default: 200
     out:
       - id: biometrics_extract_pickle
-    run: ../command_line_tools/biometrics_extract/0.2.13/biometrics_extract.cwl
+    run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl
     'sbg:x': 351.4375
     'sbg:y': 1189.28125
-  - id: biometrics_minor_0_2_13
+  - id: biometrics_minor_0_2_14
     in:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_13/biometrics_extract_pickle
+          - biometrics_extract_0_2_14/biometrics_extract_pickle
       - id: prefix
         source: prefix
       - id: plot
@@ -503,7 +503,7 @@ steps:
       - id: biometrics_minor_json
       - id: biometrics_minor_plot
       - id: biometrics_minor_sites_plot
-    run: ../command_line_tools/biometrics_minor/0.2.13/biometrics_minor.cwl
+    run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2157.875
   - id: getbasecountsmultisample_1_2_5