Merge branch 'release/1.2.5'

Author: rhshah

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2

.github/workflows/pack_cwls.yml

@@ -14,13 +14,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8.x, 3.9.x]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install cwltool
@@ -36,7 +36,7 @@ jobs:
         run: |
           echo Validating packed workflows...
           find . -name '*__packed.cwl' | xargs -I file cwltool --debug --validate file
-      - uses: EndBug/add-and-commit@v4
+      - uses: EndBug/add-and-commit@v9.1.4
         with:
           ref: ${{ github.head_ref }}
         env:

.github/workflows/validate_cwls.yml

@@ -12,19 +12,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8.x, 3.9.x]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install cwltool
         run: |
           python -m pip install toil[cwl]==5.7.1
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Validate
         run: |
           pip install cwltool

.gitignore

@@ -107,3 +107,4 @@ ENV/
 #vscode
 .vscode/*
 
+pv_vardict/pv_maf_processing.cwl

command_line_tools

@@ -317,25 +317,25 @@ outputs:
     'sbg:y': 884.875
   - id: biometrics_major_plot
     outputSource:
-      - biometrics_major_0_2_14/biometrics_major_plot
+      - biometrics_major_0_2_15/biometrics_major_plot
     type: File?
     'sbg:x': 1482.3623046875
     'sbg:y': 1496.25
   - id: biometrics_major_json
     outputSource:
-      - biometrics_major_0_2_14/biometrics_major_json
+      - biometrics_major_0_2_15/biometrics_major_json
     type: File?
     'sbg:x': 1482.3623046875
     'sbg:y': 1603.125
   - id: biometrics_major_csv
     outputSource:
-      - biometrics_major_0_2_14/biometrics_major_csv
+      - biometrics_major_0_2_15/biometrics_major_csv
     type: File
     'sbg:x': 1482.3623046875
     'sbg:y': 1710
   - id: collapsed_biometrics_extract_pickle
     outputSource:
-      - biometrics_extract_0_2_14/biometrics_extract_pickle
+      - biometrics_extract_0_2_15/biometrics_extract_pickle
     type: File
     'sbg:x': 982.1435546875
     'sbg:y': 2214.5
@@ -397,7 +397,7 @@ steps:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_14/biometrics_extract_pickle
+          - biometrics_extract_0_2_15/biometrics_extract_pickle
       - id: minor_threshold
         source: minor_threshold
       - id: prefix
@@ -414,15 +414,15 @@ steps:
       - id: biometrics_minor_json
       - id: biometrics_minor_plot
       - id: biometrics_minor_sites_plot
-    run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl
+    run: ../command_line_tools/biometrics_minor/0.2.15/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_14/biometrics_extract_pickle
+          - biometrics_extract_0_2_15/biometrics_extract_pickle
       - id: coverage_threshold
         source: coverage_threshold
       - id: prefix
@@ -435,15 +435,15 @@ steps:
       - id: biometrics_sexmismatch_csv
       - id: biometrics_sexmismatch_json
     run: >-
-      ../command_line_tools/biometrics_sexmismatch/0.2.14/biometrics_sexmismatch.cwl
+      ../command_line_tools/biometrics_sexmismatch/0.2.15/biometrics_sexmismatch.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 1760.875
-  - id: biometrics_major_0_2_14
+  - id: biometrics_major_0_2_15
     in:
       - id: input
         linkMerge: merge_nested
         source:
-          - biometrics_extract_0_2_14/biometrics_extract_pickle
+          - biometrics_extract_0_2_15/biometrics_extract_pickle
       - id: major_threshold
         source: major_threshold
       - id: prefix
@@ -458,10 +458,10 @@ steps:
       - id: biometrics_major_csv
       - id: biometrics_major_json
       - id: biometrics_major_plot
-    run: ../command_line_tools/biometrics_major/0.2.14/biometrics_major.cwl
+    run: ../command_line_tools/biometrics_major/0.2.15/biometrics_major.cwl
     'sbg:x': 982.1435546875
     'sbg:y': 2079.625
-  - id: biometrics_extract_0_2_14
+  - id: biometrics_extract_0_2_15
     in:
       - id: sample_bam
         source: collapsed_bam
@@ -482,7 +482,7 @@ steps:
         source: collapsed_biometrics_extract_file_type
     out:
       - id: biometrics_extract_pickle
-    run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl
+    run: ../command_line_tools/biometrics_extract/0.2.15/biometrics_extract.cwl
     'sbg:x': 351.4375
     'sbg:y': 1328.9375
   - id: getbasecountsmultisample_1_2_5