diff --git a/.github/workflows/test-snake.yml b/.github/workflows/test-snake.yml index 18be5b0..5dc7034 100644 --- a/.github/workflows/test-snake.yml +++ b/.github/workflows/test-snake.yml @@ -51,15 +51,8 @@ jobs: with: directory: '.test' snakefile: 'workflow/Snakefile' - args: '--cores 1 --use-conda --conda-cleanup-pkgs cache' + args: '--cores 1 --use-conda --conda-frontend mamba --conda-cleanup-pkgs cache' stagein: | - source $GITHUB_WORKSPACE/.venv/bin/activate - export PYTHONPATH="${PYTHONPATH}:$GITHUB_WORKSPACE:$GITHUB_WORKSPACE/src" + export PYTHONPATH="${PYTHONPATH}:/github/workspace:/github/workspace/src" echo $PYTHONPATH - which python - python --version - pip list - python -c "import sys; print(sys.path)" - python -c "import usefulgnom; print(usefulgnom.__file__)" - python -c "import snakemake; print(snakemake.__file__)" show-disk-usage-on-error: true \ No newline at end of file diff --git a/environment.yml b/environment.yml index 38349a7..3579c74 100644 --- a/environment.yml +++ b/environment.yml @@ -9,4 +9,10 @@ channels: dependencies: - python=3.11.2 - snakemake=8.18.2 - - poetry=1.8.3 \ No newline at end of file + - poetry=1.8.3 + - matplotlib=3.9.2 + - pandas=2.2.2 + - seaborn=0.13.2 + - pip + - pip: + - -e . \ No newline at end of file diff --git a/src/usefulgnom/analyze/basecnt_coverage.py b/src/usefulgnom/analyze/basecnt_coverage.py index d81d2f1..932db75 100644 --- a/src/usefulgnom/analyze/basecnt_coverage.py +++ b/src/usefulgnom/analyze/basecnt_coverage.py @@ -1,4 +1,5 @@ -"""Implements the read coverage analysis. +""" + Implements the read coverage analysis. Credits: - core code: @AugusteRi (arimaite@ethz.ch) diff --git a/workflow/Snakefile b/workflow/Snakefile index 83eacf3..af6c1b1 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -5,6 +5,9 @@ configfile: "../config/config.yaml" include: "rules/base_coverage.smk" include: "rules/smk_testing.smk" +conda: + "../environment.yml" + rule all: input: "../results/statistics.csv" \ No newline at end of file