diff --git a/src/qualimap/qualimap_rnaseq/config.vsh.yaml b/src/qualimap/qualimap_rnaseq/config.vsh.yaml index adb3a5a3..35e8c6ff 100644 --- a/src/qualimap/qualimap_rnaseq/config.vsh.yaml +++ b/src/qualimap/qualimap_rnaseq/config.vsh.yaml @@ -93,23 +93,11 @@ test_resources: engines: - type: docker - image: ubuntu:22.04 + image: quay.io/biocontainers/qualimap:2.3--hdfd78af_0 setup: - - type: apt - packages: [ r-base, unzip, wget, openjdk-8-jdk, libxml2-dev, libcurl4-openssl-dev ] - type: docker run: | - wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && \ - unzip qualimap_v2.3.zip && \ - cp -a qualimap_v2.3/. usr/bin && \ - unset DISPLAY && \ - mkdir -p tmp && \ - export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp && \ - echo "qualimap: v2.3" > /var/software_versions.txt - - - type: r - bioc: [ NOISeqr ] - cran: [ optparse ] + echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') runners: - type: executable - type: nextflow