diff --git a/config/nxf_call_str.config b/config/nxf_call_str.config index b0c828ed4..40b4cfb6c 100644 --- a/config/nxf_call_str.config +++ b/config/nxf_call_str.config @@ -2,7 +2,7 @@ includeConfig 'nxf.config' env { CMD_EXPANSIONHUNTER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/expansionhunter-5.0.0.sif ExpansionHunter" - CMD_STRAGLR="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/straglr-1.4.4_vip_v2.sif straglr-genotype" + CMD_STRAGLR="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/straglr-1.4.4_vip_v3.sif straglr-genotype" } params { diff --git a/config/nxf_vcf.config b/config/nxf_vcf.config index 4243a9bc0..8c0ebad62 100644 --- a/config/nxf_vcf.config +++ b/config/nxf_vcf.config @@ -8,7 +8,7 @@ env { CMD_FILTERVEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-111.0.sif filter_vep" 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-6.0.2.sif" - CMD_VCFDECISIONTREE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.0.0.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" // workaround for SAMtools https://github.com/samtools/samtools/issues/1366#issuecomment-769170935 diff --git a/install.sh b/install.sh index 97bbbedd1..a7250a16a 100755 --- a/install.sh +++ b/install.sh @@ -82,9 +82,9 @@ download_files() { urls+=("7486bd5de526d9888df8eea2d8bdea48" "images/minimap2-2.27.sif") urls+=("06ac8a76a307fa42fffd80ab906fd24b" "images/picard-3.1.1.sif") urls+=("9a4b685b26744113d3ea0a3904c02706" "images/samtools-1.17-patch1.sif") - urls+=("556d7e6b523e282f9920729edc3d0842" "images/straglr-1.4.4_vip_v2.sif") + urls+=("8f6e06847776448e004df8b863571109" "images/straglr-1.4.4_vip_v3.sif") urls+=("bcc157242cd9b09c66f015c52ef2d61d" "images/stranger-0.8.1.sif") - urls+=("4fbbd8642ead7754cb8cc19740e18175" "images/vcf-decision-tree-4.0.0.sif") + urls+=("57401e7b835fed2f52fafadc0dd744d4" "images/vcf-decision-tree-4.1.1.sif") urls+=("9c4d7b48138f29651cdd45eb8d0cc4b6" "images/vcf-inheritance-matcher-3.1.0.sif") urls+=("7f3c5115f68998067a404c922b2e3b15" "images/vcf-report-6.0.2.sif") urls+=("7bffc236a7c65b2b2e2e5f7d64beaa87" "images/vep-111.0.sif") diff --git a/utils/apptainer/build.sh b/utils/apptainer/build.sh index fee225a66..2e399ee9b 100644 --- a/utils/apptainer/build.sh +++ b/utils/apptainer/build.sh @@ -93,8 +93,8 @@ main() { images+=("picard-3.1.1") images+=("samtools-1.17-patch1") images+=("stranger-0.8.1") - images+=("straglr-1.4.4_vip_v2") - images+=("vcf-decision-tree-4.0.0") + images+=("straglr-1.4.4_vip_v3") + images+=("vcf-decision-tree-4.1.1") images+=("vcf-inheritance-matcher-3.1.0") images+=("vcf-report-6.0.2") diff --git a/utils/apptainer/def/straglr-1.4.4_vip_v2.def b/utils/apptainer/def/straglr-1.4.4_vip_v3.def similarity index 76% rename from utils/apptainer/def/straglr-1.4.4_vip_v2.def rename to utils/apptainer/def/straglr-1.4.4_vip_v3.def index dfccf6959..70f89de91 100644 --- a/utils/apptainer/def/straglr-1.4.4_vip_v2.def +++ b/utils/apptainer/def/straglr-1.4.4_vip_v3.def @@ -11,8 +11,8 @@ From: sif/build/ubuntu-22.04.sif curl -Ls -o /opt/trf/trf "https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64" chmod +x /opt/trf/trf - #3e9fbcb77984617151d4010fee087ea423d998f9 == v1.4.4_vip_v2 - pip install git+https://github.com/molgenis/straglr.git@3e9fbcb77984617151d4010fee087ea423d998f9#egg=straglr + #fef64d4240293df0ddae0a190fb20c5ed9c6c129 == v1.4.4_vip_v3 + pip install git+https://github.com/molgenis/straglr.git@fef64d4240293df0ddae0a190fb20c5ed9c6c129#egg=straglr # cleanup pip cache purge diff --git a/utils/apptainer/def/vcf-decision-tree-4.0.0.def b/utils/apptainer/def/vcf-decision-tree-4.1.1.def similarity index 80% rename from utils/apptainer/def/vcf-decision-tree-4.0.0.def rename to utils/apptainer/def/vcf-decision-tree-4.1.1.def index 1d1d41a20..3e9e6698d 100644 --- a/utils/apptainer/def/vcf-decision-tree-4.0.0.def +++ b/utils/apptainer/def/vcf-decision-tree-4.1.1.def @@ -7,8 +7,8 @@ From: sif/build/openjdk-17.sif %post version_major=4 - version_minor=0 - version_patch=0 + version_minor=1 + version_patch=1 # install apk update @@ -16,7 +16,7 @@ From: sif/build/openjdk-17.sif mkdir -p /opt/vcf-decision-tree/lib curl -Ls -o /opt/vcf-decision-tree/lib/vcf-decision-tree.jar "https://github.com/molgenis/vip-decision-tree/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-decision-tree.jar" - echo "4029e1d488478a1e71214b352ef17b088bbb9ba3eff86036ef5e0fdf60fad33e /opt/vcf-decision-tree/lib/vcf-decision-tree.jar" | sha256sum -c + echo "5c18aa3c302bbc4120c0fae50bca99828f7304837a52d96606bea0133a140780 /opt/vcf-decision-tree/lib/vcf-decision-tree.jar" | sha256sum -c # cleanup apk del .build-dependencies diff --git a/vip.sh b/vip.sh index 20443bd37..d34c8c6a6 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:-"${SCRIPT_DIR}"}" -VIP_VERSION="7.7.0" +VIP_VERSION="7.7.1" display_version() { echo -e "${VIP_VERSION}"