diff --git a/modules/local/virusbreakend/Dockerfile b/modules/local/virusbreakend/Dockerfile new file mode 100644 index 00000000..f8cc9d06 --- /dev/null +++ b/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}" diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf index 64195c3c..da93d763 100644 --- a/modules/local/virusbreakend/main.nf +++ b/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)