diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 4af547eee..2c4e4e8ab 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -4,11 +4,10 @@ on: [push, pull_request] jobs: build: - runs-on: ubuntu-latest strategy: matrix: - python-version: [3.6, 3.7, 3.8] + python-version: [3.8.17, 3.10.12, 3.11.4] steps: - uses: actions/checkout@v2 diff --git a/janis_bioinformatics/__meta__.py b/janis_bioinformatics/__meta__.py index 12826eda8..626494abb 100644 --- a/janis_bioinformatics/__meta__.py +++ b/janis_bioinformatics/__meta__.py @@ -1,2 +1,2 @@ -__version__ = "v0.11.4" +__version__ = "v0.12.1" description = "Bioinformatics tools for Janis; the Pipeline creation helper" diff --git a/janis_bioinformatics/tools/bcftools/view/base.py b/janis_bioinformatics/tools/bcftools/view/base.py index 2804ad4f2..d04477dcf 100644 --- a/janis_bioinformatics/tools/bcftools/view/base.py +++ b/janis_bioinformatics/tools/bcftools/view/base.py @@ -92,7 +92,7 @@ def memory(self, hints: Dict[str, Any]): def inputs(self) -> List[ToolInput]: return [ ToolInput("file", CompressedVcf(), position=2), - ToolInput("outputFilename", Filename, prefix=">", position=5) + ToolInput("outputFilename", Filename, prefix=">", position=5), * self.additional_inputs, ] diff --git a/janis_bioinformatics/tools/common/indexfasta.py b/janis_bioinformatics/tools/common/indexfasta.py index 0fdc4d721..31f5ff55b 100644 --- a/janis_bioinformatics/tools/common/indexfasta.py +++ b/janis_bioinformatics/tools/common/indexfasta.py @@ -114,6 +114,9 @@ def constructor(self): ) self.output("out_dict", source=self.create_dict, output_name="reference") + def skip_test(cls) -> bool: + return True + def bind_metadata(self): return ToolMetadata( contributors=["Michael Franklin"], diff --git a/janis_bioinformatics/tools/pmac/circosplot/base.py b/janis_bioinformatics/tools/pmac/circosplot/base.py index c9c1a128f..0e7a49a31 100644 --- a/janis_bioinformatics/tools/pmac/circosplot/base.py +++ b/janis_bioinformatics/tools/pmac/circosplot/base.py @@ -97,6 +97,9 @@ def cpus(self, hints: Dict[str, Any]): return val return 1 + def skip_test(cls) -> bool: + return True + def bind_metadata(self) -> ToolMetadata: from datetime import datetime diff --git a/tests/__init__.py b/tests/__init__.py index e69de29bb..c5eaea245 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1,2 @@ +import collections +collections.Callable = collections.abc.Callable