From d3ca38a4d165c3f0e8432be89410fddb3f08b0bb Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Wed, 21 Jun 2023 15:17:25 -0500 Subject: [PATCH 1/2] Use enums for inputs that are passed to enums. --- definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl | 5 ++++- definitions/subworkflows/cram_to_cnvkit.cwl | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl b/definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl index 1537d435b..aebc05e57 100644 --- a/definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl +++ b/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: diff --git a/definitions/subworkflows/cram_to_cnvkit.cwl b/definitions/subworkflows/cram_to_cnvkit.cwl index 362a0ed50..1e314ae9e 100644 --- a/definitions/subworkflows/cram_to_cnvkit.cwl +++ b/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: From 3c948c963f11ac937f4c44b5e03db1bd857e56ca Mon Sep 17 00:00:00 2001 From: Thomas Mooney Date: Wed, 21 Jun 2023 15:27:39 -0500 Subject: [PATCH 2/2] Update to cwltool==3.1.20230601100705 --- .github/workflows/main.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2a1e2508e..83f578a37 100644 --- a/.github/workflows/main.yml +++ b/.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