Merge pull request genome#1086 from tmooney/update_cwltool

Update python and cwltool version for testing CWL syntax

.github/workflows/main.yml

@@ -20,15 +20,12 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install 'setuptools>=18.5'
-          python -m pip install 'cwltool==1.0.20181217162649'
-          python -m pip install 'ruamel.yaml==0.15.77'
-          python -m pip install 'mdutils==1.0.0'
-          python -m pip install 'PyYAML==5.1.2'
+          python -m pip install 'cwltool==3.1.20230601100705'
+          python -m pip install 'ruamel.yaml==0.17.27'
       - name: Run cwltool validate
         run: |
           cd $GITHUB_WORKSPACE/definitions

definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl

@@ -59,7 +59,10 @@ inputs:
     gene_transcript_lookup_table:
        type: File
     strand:
-       type: string?
+       type:
+          - "null"
+          - type: enum
+            symbols: ["first", "second", "unstranded"]
     refFlat:
         type: File
     ribosomal_intervals:

definitions/subworkflows/cram_to_cnvkit.cwl

@@ -17,7 +17,10 @@ inputs:
     access:
         type: File?
     method:
-        type: string?
+        type:
+            - "null"
+            - type: enum
+              symbols: ["hybrid", "amplicon", "wgs"]
     diagram:
         type: boolean?
     scatter_plot: