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bump VEP 111.0 to 112.0 #615

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bump VEP 111.0 to 112.0 #615

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a5eafff
bump VEP 111.0 to 112.0
dennishendriksen Jun 10, 2024
e35c026
install VEP 112 db
dennishendriksen Jun 10, 2024
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2 changes: 1 addition & 1 deletion config/nxf.config
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Expand Up @@ -8,7 +8,7 @@ env {

// tools used by multiple workflows
CMD_BCFTOOLS = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/bcftools-1.17.sif bcftools"
CMD_BGZIP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-111.0.sif bgzip"
CMD_BGZIP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-112.0.sif bgzip"
CMD_GLNEXUS="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/glnexus_v1.4.5-patched.sif glnexus_cli"
CMD_PICARD = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/picard-3.1.1.sif"
CMD_SAMTOOLS= "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/samtools-1.17-patch1.sif samtools"
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4 changes: 2 additions & 2 deletions config/nxf_vcf.config
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Expand Up @@ -4,8 +4,8 @@ env {
CMD_ANNOTSV = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/annotsv-3.3.6.sif AnnotSV"
CMD_CAPICE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/capice-5.1.2.sif capice"
CMD_GADO = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/gado-1.0.3.sif"
CMD_VEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-111.0.sif vep"
CMD_FILTERVEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-111.0.sif filter_vep"
CMD_VEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-112.0.sif vep"
CMD_FILTERVEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-112.0.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} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.1.1.sif"
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8 changes: 4 additions & 4 deletions install.sh
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Expand Up @@ -88,7 +88,7 @@ download_files() {
urls+=("57401e7b835fed2f52fafadc0dd744d4" "images/vcf-decision-tree-4.1.1.sif")
urls+=("9c4d7b48138f29651cdd45eb8d0cc4b6" "images/vcf-inheritance-matcher-3.1.0.sif")
urls+=("7f3c5115f68998067a404c922b2e3b15" "images/vcf-report-6.0.2.sif")
urls+=("7bffc236a7c65b2b2e2e5f7d64beaa87" "images/vep-111.0.sif")
urls+=("24d98b0e5f05267fe212e56f319dedb0" "images/vep-112.0.sif")
urls+=("82be3c18406e7c027ee4cec83a723d71" "nextflow-24.04.2-all")
if [ "${assembly}" == "ALL" ] || [ "${assembly}" == "GRCh37" ]; then
urls+=("11b8eb3d28482729dd035458ad5bda01" "resources/GRCh37/human_g1k_v37.fasta.gz")
Expand Down Expand Up @@ -139,7 +139,7 @@ download_files() {
urls+=("42e31fe6e3502fb9bc0b14121f0f844b" "resources/hpo_20240404.tsv")
# update utils/install.sh when updating inheritance.tsv
urls+=("df31eb0fe9ebd9ae26c8d6f5f7ba6e57" "resources/inheritance_20240115.tsv")
urls+=("7138e76a38d6f67935699d06082ecacf" "resources/vep/cache/homo_sapiens_refseq_vep_111_GRCh38.tar.gz")
urls+=("9c05a34b974afd404deeef31d1ca1c30" "resources/vep/cache/homo_sapiens_refseq_vep_112_GRCh38.tar.gz")
# when modifying urls array, please keep list in 'ls -l' order

for ((i = 0; i < ${#urls[@]}; i += 2)); do
Expand All @@ -158,8 +158,8 @@ extract_files() {
fi

local -r vep_dir="${output_dir}/resources/vep/cache"
if [ ! -d "${vep_dir}/homo_sapiens_refseq/111_GRCh38" ]; then
local -r vep_gz="${vep_dir}/homo_sapiens_refseq_vep_111_GRCh38.tar.gz"
if [ ! -d "${vep_dir}/homo_sapiens_refseq/112_GRCh38" ]; then
local -r vep_gz="${vep_dir}/homo_sapiens_refseq_vep_112_GRCh38.tar.gz"
echo -e "extracting ${vep_gz} ..."
tar -xzf "${vep_gz}" -C "${vep_dir}"
fi
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2 changes: 1 addition & 1 deletion utils/apptainer/build.sh
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Expand Up @@ -106,7 +106,7 @@ main() {
done

declare -A uris
uris["docker://ensemblorg/ensembl-vep:release_111.0"]="vep-111.0"
uris["docker://ensemblorg/ensembl-vep:release_112.0"]="vep-112.0"
uris["docker://google/deepvariant:1.6.1"]="deepvariant-1.6.1"
uris["docker://google/deepvariant:deeptrio-1.6.1"]="deepvariant_deeptrio-1.6.1"

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4 changes: 2 additions & 2 deletions utils/create_gnomad.sh
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Expand Up @@ -5,8 +5,8 @@ SCRIPT_DIR=$(dirname "$(realpath "$0")")

APPTAINER_CACHEDIR="put_your_dir_here"
CMD_BCFTOOLS="apptainer exec --no-mount home --bind /groups ${APPTAINER_CACHEDIR}/bcftools-1.19.sif bcftools"
CMD_BGZIP="apptainer exec --no-mount home --bind /groups ${APPTAINER_CACHEDIR}/vep-111.0.sif bgzip"
CMD_TABIX="apptainer exec --no-mount home --bind /groups ${APPTAINER_CACHEDIR}/vep-111.0.sif tabix"
CMD_BGZIP="apptainer exec --no-mount home --bind /groups ${APPTAINER_CACHEDIR}/vep-112.0.sif bgzip"
CMD_TABIX="apptainer exec --no-mount home --bind /groups ${APPTAINER_CACHEDIR}/vep-112.0.sif tabix"

THREADS=4

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