From b74993e281b912aeecb4f1fb3053b981b6c6f5fe Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Mon, 21 Aug 2023 11:58:15 -0400 Subject: [PATCH] Update docker and pipelines --- containers/azimuth/Dockerfile | 2 +- containers/azimuth/pipeline.cwl | 4 +++- containers/celltypist/Dockerfile | 2 +- containers/celltypist/pipeline.cwl | 4 +++- containers/extract-summary/Dockerfile | 2 +- containers/extract-summary/pipeline.cwl | 4 +++- containers/popv/Dockerfile | 2 +- containers/popv/pipeline.cwl | 4 +++- containers/preprocess/Dockerfile | 2 +- containers/preprocess/pipeline.cwl | 4 +++- 10 files changed, 20 insertions(+), 10 deletions(-) diff --git a/containers/azimuth/Dockerfile b/containers/azimuth/Dockerfile index 7dc880d..cf12acf 100644 --- a/containers/azimuth/Dockerfile +++ b/containers/azimuth/Dockerfile @@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt COPY context/* . -ENTRYPOINT ["python3", "/main.py"] \ No newline at end of file +CMD ["python3", "/main.py"] \ No newline at end of file diff --git a/containers/azimuth/pipeline.cwl b/containers/azimuth/pipeline.cwl index 488cc8b..75ca43c 100644 --- a/containers/azimuth/pipeline.cwl +++ b/containers/azimuth/pipeline.cwl @@ -9,7 +9,9 @@ requirements: types: - $import: ./options.yml -baseCommand: python3 /main.py +baseCommand: python3 +arguments: + - /main.py inputs: matrix: diff --git a/containers/celltypist/Dockerfile b/containers/celltypist/Dockerfile index 95e2fc6..ef436de 100644 --- a/containers/celltypist/Dockerfile +++ b/containers/celltypist/Dockerfile @@ -8,4 +8,4 @@ RUN python -c "import celltypist; celltypist.models.download_models()" COPY context/* . -ENTRYPOINT ["python", "/main.py"] \ No newline at end of file +CMD ["python", "/main.py"] \ No newline at end of file diff --git a/containers/celltypist/pipeline.cwl b/containers/celltypist/pipeline.cwl index 1442ee2..b9590cc 100644 --- a/containers/celltypist/pipeline.cwl +++ b/containers/celltypist/pipeline.cwl @@ -9,7 +9,9 @@ requirements: types: - $import: ./options.yml -baseCommand: python /main.py +baseCommand: python +arguments: + - /main.py inputs: matrix: diff --git a/containers/extract-summary/Dockerfile b/containers/extract-summary/Dockerfile index aa850e9..a7588b2 100644 --- a/containers/extract-summary/Dockerfile +++ b/containers/extract-summary/Dockerfile @@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt COPY context/* . -ENTRYPOINT ["python", "/main.py"] +CMD ["python", "/main.py"] diff --git a/containers/extract-summary/pipeline.cwl b/containers/extract-summary/pipeline.cwl index 8238925..861f891 100644 --- a/containers/extract-summary/pipeline.cwl +++ b/containers/extract-summary/pipeline.cwl @@ -9,7 +9,9 @@ requirements: types: - $import: ./options.yml -baseCommand: python /main.py +baseCommand: python +arguments: + - /main.py inputs: annotations: diff --git a/containers/popv/Dockerfile b/containers/popv/Dockerfile index 5fddb58..dba4287 100644 --- a/containers/popv/Dockerfile +++ b/containers/popv/Dockerfile @@ -14,4 +14,4 @@ RUN pip install -r requirements-freeze.txt COPY context/* . -ENTRYPOINT ["python", "/main.py"] +CMD ["python", "/main.py"] diff --git a/containers/popv/pipeline.cwl b/containers/popv/pipeline.cwl index a558d45..c5fc5e8 100644 --- a/containers/popv/pipeline.cwl +++ b/containers/popv/pipeline.cwl @@ -9,7 +9,9 @@ requirements: types: - $import: ./options.yml -baseCommand: python /main.py +baseCommand: python +arguments: + - /main.py inputs: matrix: diff --git a/containers/preprocess/Dockerfile b/containers/preprocess/Dockerfile index be1d754..5d0bd8c 100644 --- a/containers/preprocess/Dockerfile +++ b/containers/preprocess/Dockerfile @@ -5,4 +5,4 @@ RUN pip install -r requirements-freeze.txt COPY context/* . -ENTRYPOINT ["python", "/main.py"] \ No newline at end of file +CMD ["python", "/main.py"] \ No newline at end of file diff --git a/containers/preprocess/pipeline.cwl b/containers/preprocess/pipeline.cwl index 163754c..60f01ff 100644 --- a/containers/preprocess/pipeline.cwl +++ b/containers/preprocess/pipeline.cwl @@ -9,7 +9,9 @@ requirements: types: - $import: ./options.yml -baseCommand: python /main.py +baseCommand: python +arguments: + - /main.py inputs: matrix: