use FROM ghcr.io/pangenome/pggb:latest

Dockerfile

@@ -1,15 +1,35 @@
-FROM nfcore/base:dev
-LABEL authors="Simon Heumos, Michael L Heuer" \
+FROM ghcr.io/pangenome/pggb:latest
+LABEL authors="Simon Heumos, Michael Heuer, Lukas Heumos, Erik Garrison, Andrea Guarracino" \
       description="Docker image containing all software requirements for the nf-core/pangenome pipeline"
 
+# Install procps so that Nextflow can poll CPU usage and
+# deep clean the apt cache to reduce image/layer size
+RUN apt-get update \
+    && apt-get install -y wget \
+                          procps \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+# Install miniconda
+RUN wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-latest-Linux-x86_64.sh
+
+# Add conda to the path
+ENV PATH /root/miniconda3/bin:$PATH
+
 # Install the conda environment
 COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
 ENV PATH /opt/conda/envs/nf-core-pangenome-1.0dev/bin:$PATH
 
-# Dump the details of the installed packages to a file for posterity
+# Set path for all users
+RUN echo "export PATH=$PATH" > /etc/profile
+
+# Dump the details of the conda-installed packages to a file for posterity
 RUN conda env export --name nf-core-pangenome-1.0dev > nf-core-pangenome-1.0dev.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version

environment.yml

@@ -14,5 +14,4 @@ dependencies:
   - conda-forge::pygments=2.6.1
 
   ## bioconda packages
-  - bioconda::fastqc=0.11.9
   - bioconda::multiqc=1.9