diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e72bff5..f4cf939 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -24,7 +24,7 @@ jobs: steps: - uses: actions/checkout@v1 - name: Setup workflow environment - run: make conda-tests + run: make conda-install - name: Scripts unit-testing run: make all-unit-tests - name: Run Snakemake-workflow diff --git a/Snakefile b/Snakefile index 2226bc1..9e2ec8c 100644 --- a/Snakefile +++ b/Snakefile @@ -6,7 +6,7 @@ if sys.version_info < (3, 8): raise SystemError("Please use Python 3.8 or later.") # Snakemake 5.14.0 at least is required -snakemake.utils.min_version("5.14.0") +snakemake.utils.min_version("5.20.1") include: "rules/common.smk" include: "rules/copy.smk" diff --git a/envs/workflows.yaml b/envs/workflows.yaml index 2aa2002..46e879f 100644 --- a/envs/workflows.yaml +++ b/envs/workflows.yaml @@ -5,15 +5,19 @@ channels: - conda-forge - defaults dependencies: - - conda-forge::python=3.8.2 - - conda-forge::pytest=5.4.1 + - conda-forge::python=3.8.5 + - conda-forge::pytest=5.4.3 - conda-forge::datrie=0.8.2 - - conda-forge::git=2.26.0 - - conda-forge::jinja2=2.11.1 + - conda-forge::git=2.27.0 + - conda-forge::jinja2=2.11.2 - conda-forge::pygraphviz=1.5 - - conda-forge::flask=1.1.1 - - conda-forge::pandas=1.0.3 + - conda-forge::flask=1.1.2 + - conda-forge::pandas=1.0.5 - conda-forge::zlib=1.2.11 - - conda-forge::openssl=1.1.1e + - conda-forge::openssl=1.1.1g - conda-forge::networkx=2.4 - - bioconda::snakemake=5.14.0 + - bioconda::snakemake=5.20.1 + - conda-forge::ipython=7.16.1 + - conda-forge::bashlex=0.15 + - conda-forge::black=19.10b0 + - conda-forge::patsy=0.5.1