diff --git a/config/nxf_vcf.config b/config/nxf_vcf.config index 45bb5cb73..f08850a75 100644 --- a/config/nxf_vcf.config +++ b/config/nxf_vcf.config @@ -9,7 +9,7 @@ env { CMD_STRANGER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/stranger-0.8.1.sif stranger" CMD_VCFREPORT="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-7.0.0.sif" CMD_VCFDECISIONTREE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.1.1.sif" - CMD_VCFINHERITANCEMATCHER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-3.1.0.sif" + CMD_VCFINHERITANCEMATCHER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-3.1.1.sif" // workaround for SAMtools https://github.com/samtools/samtools/issues/1366#issuecomment-769170935 REF_PATH = ":" diff --git a/install.sh b/install.sh index ad557f3ff..94b5d61aa 100755 --- a/install.sh +++ b/install.sh @@ -88,7 +88,7 @@ download_files() { urls+=("8f6e06847776448e004df8b863571109" "images/straglr-1.4.4_vip_v3.sif") urls+=("bcc157242cd9b09c66f015c52ef2d61d" "images/stranger-0.8.1.sif") urls+=("57401e7b835fed2f52fafadc0dd744d4" "images/vcf-decision-tree-4.1.1.sif") - urls+=("9c4d7b48138f29651cdd45eb8d0cc4b6" "images/vcf-inheritance-matcher-3.1.0.sif") + urls+=("231b9369cdfdb080455a3eddb2e0019b" "images/vcf-inheritance-matcher-3.1.1.sif") urls+=("53f9265acb2041b2b93c692177d91d74" "images/vcf-report-7.0.0.sif") urls+=("7bffc236a7c65b2b2e2e5f7d64beaa87" "images/vep-111.0.sif") urls+=("82be3c18406e7c027ee4cec83a723d71" "nextflow-24.04.2-all") diff --git a/utils/apptainer/build.sh b/utils/apptainer/build.sh index cfdacdbf1..da05e73a7 100644 --- a/utils/apptainer/build.sh +++ b/utils/apptainer/build.sh @@ -97,7 +97,7 @@ main() { images+=("stranger-0.8.1") images+=("straglr-1.4.4_vip_v3") images+=("vcf-decision-tree-4.1.1") - images+=("vcf-inheritance-matcher-3.1.0") + images+=("vcf-inheritance-matcher-3.1.1") images+=("vcf-report-7.0.0") for i in "${!images[@]}"; do diff --git a/utils/apptainer/def/vcf-inheritance-matcher-3.1.0.def b/utils/apptainer/def/vcf-inheritance-matcher-3.1.1.def similarity index 84% rename from utils/apptainer/def/vcf-inheritance-matcher-3.1.0.def rename to utils/apptainer/def/vcf-inheritance-matcher-3.1.1.def index fb052a710..7c012609f 100644 --- a/utils/apptainer/def/vcf-inheritance-matcher-3.1.0.def +++ b/utils/apptainer/def/vcf-inheritance-matcher-3.1.1.def @@ -8,7 +8,7 @@ From: sif/build/openjdk-17.sif %post version_major=3 version_minor=1 - version_patch=0 + version_patch=1 # install apk update @@ -16,7 +16,7 @@ From: sif/build/openjdk-17.sif mkdir -p /opt/vcf-inheritance-matcher/lib curl -Ls -o /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar "https://github.com/molgenis/vip-inheritance-matcher/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-inheritance-matcher.jar" - echo "1b4b9f33542ce0e19c7bc22542e857137ca12f2e62f68f4d7f0254da43f2143b /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar" | sha256sum -c + echo "f7afe980c217efe7b5b5ec932c1bf885f4e812e7814b2b58bf002db98a3c58a2 /opt/vcf-inheritance-matcher/lib/vcf-inheritance-matcher.jar" | sha256sum -c # cleanup apk del .build-dependencies diff --git a/vip.sh b/vip.sh index 7837edcb9..f55a35abe 100755 --- a/vip.sh +++ b/vip.sh @@ -7,7 +7,7 @@ SCRIPT_NAME="$(basename "$0")" # SCRIPT_DIR is incorrect when vip.sh is submitted as a Slurm job that is submitted as part of another Slurm job VIP_DIR="${VIP_DIR:-"${SCRIPT_DIR}"}" -VIP_VERSION="7.9.0" +VIP_VERSION="7.9.1" display_version() { echo -e "${VIP_VERSION}"