Merge pull request #12 from nf-core/nf-core-gridss-docker-image

Use fixed GRIDSS container for VIRUSBreakend

modules/local/virusbreakend/Dockerfile

@@ -0,0 +1,34 @@
+FROM continuumio/miniconda3:23.5.2-0-alpine as build
+
+RUN \
+    conda install conda-libmamba-solver
+
+RUN \
+    echo -e > ~/.condarc '\
+solver: libmamba\n\
+channels:\n\
+    - conda-forge\n\
+    - bioconda\n\
+    - defaults'
+
+RUN \
+    conda create -y -p /env/ \
+        'gridss=2.13.2=h50ea8bc_3' \
+        'grep'
+
+# Install Dfam database required for RepeatMasker
+RUN \
+    conda install -y curl && \
+    curl -s https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz | \
+        gzip -cd > /env/share/RepeatMasker/Libraries/Dfam.h5
+
+RUN \
+    conda clean -yaf
+
+# Move Conda environment into standard BioContainers base image
+FROM quay.io/bioconda/base-glibc-busybox-bash:2.1.0
+
+COPY --from=build /env/ /env/
+
+ENV PATH="/env/bin:${PATH}"
+ENV LD_LIBRARY_PATH="/env/lib/:${LD_LIBRARY_PATH}"

modules/local/virusbreakend/main.nf

@@ -5,9 +5,7 @@ process VIRUSBREAKEND {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gridss:2.13.2--h50ea8bc_3':
-        'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"
+    container "nf-core/gridss:2.13.2--1"
 
     input:
     tuple val(meta), path(bam)