update workflow to build Docker from current checkout

.github/workflows/docker-publish.yml

@@ -50,7 +50,8 @@ jobs:
         id: build-and-push
         uses: docker/build-push-action@v6
         with:
-          context: src/docker
+          context: .
+          file: ./src/docker/Dockerfile
           tags: ${{ steps.meta.outputs.tags }}
           push: true
           labels: ${{ steps.meta.outputs.labels }}

src/docker/Dockerfile

@@ -8,16 +8,14 @@ RUN mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake=6.10.0
 RUN  echo "source activate snakemake" > ~/.bashrc
 ENV PATH=/opt/conda/envs/snakemake/bin:$PATH
 
-WORKDIR /Marker_pipeline
-
 RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y \
          locales \
          libtbb2 \
          unzip \
     && rm -rf /var/lib/apt/lists/*
 
-RUN git clone https://github.com/CobiontID/Marker-pipeline.git . && \
-    sed -i 's/dependencies:/dependencies:\n  - python=3.9/' envs/hifiasm.yaml && \
-    sed -i '/- defaults/d'  envs/hifiasm.yaml
+WORKDIR /Marker_pipeline
+
+COPY . .
 
-RUN snakemake -p --cores 1 --use-conda --conda-prefix /opt/conda/envs --conda-create-envs-only -s  /MarkerScanPipeline/create-envs.smk
+RUN snakemake -p --cores 1 --use-conda --conda-prefix /opt/conda/envs --conda-create-envs-only -s create-envs.smk