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https://github.com/MillironX/nf-core_modules.git
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update ensemblvep to 106.1 and cache to 106 (#1876)
This commit is contained in:
Maxime U. Garcia
GitHub
parent
b6ed584443
commit
973151e9ea
6 changed files with 31 additions and 31 deletions
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@ -11,11 +11,11 @@ RUN conda env create -f /environment.yml && conda clean -a
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# Setup default ARG variables
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ARG GENOME=GRCh38
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ARG SPECIES=homo_sapiens
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ARG VEP_VERSION=105
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ARG VEP_TAG=105.0
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ARG VEP_CACHE_VERSION=106
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ARG VEP_VERSION=106.1
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# Add conda installation dir to PATH (instead of doing 'conda activate')
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ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-vep-${VEP_VERSION}/bin:$PATH
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# Download Genome
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RUN vep_install \
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@ -23,9 +23,9 @@ RUN vep_install \
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-c .vep \
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-s ${SPECIES} \
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-y ${GENOME} \
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--CACHE_VERSION ${VEP_VERSION} \
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--CACHE_VERSION ${VEP_CACHE_VERSION} \
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--CONVERT \
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--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
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# Dump the details of the installed packages to a file for posterity
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RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml
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RUN conda env export --name nf-core-vep-${VEP_VERSION} > nf-core-vep-${VEP_VERSION}.yml
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@ -6,23 +6,23 @@ set -euo pipefail
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build_push() {
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GENOME=$1
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SPECIES=$2
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VEP_VERSION=$3
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VEP_TAG=$4
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VEP_CACHE_VERSION=$3
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VEP_VERSION=$4
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docker build \
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. \
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-t nfcore/vep:${VEP_TAG}.${GENOME} \
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-t nfcore/vep:${VEP_VERSION}.${GENOME} \
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--build-arg GENOME=${GENOME} \
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--build-arg SPECIES=${SPECIES} \
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--build-arg VEP_VERSION=${VEP_VERSION} \
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--build-arg VEP_TAG=${VEP_TAG}
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--build-arg VEP_CACHE_VERSION=${VEP_CACHE_VERSION} \
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--build-arg VEP_VERSION=${VEP_VERSION}
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docker push nfcore/vep:${VEP_TAG}.${GENOME}
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docker push nfcore/vep:${VEP_VERSION}.${GENOME}
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}
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build_push "GRCh37" "homo_sapiens" "105" "105.0"
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build_push "GRCh38" "homo_sapiens" "105" "105.0"
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build_push "GRCm38" "mus_musculus" "102" "105.0"
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build_push "GRCm39" "mus_musculus" "105" "105.0"
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build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
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build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"
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build_push "GRCh37" "homo_sapiens" "106" "106.1"
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build_push "GRCh38" "homo_sapiens" "106" "106.1"
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build_push "GRCm38" "mus_musculus" "102" "106.1"
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build_push "GRCm39" "mus_musculus" "106" "106.1"
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build_push "CanFam3.1" "canis_lupus_familiaris" "104" "106.1"
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build_push "WBcel235" "caenorhabditis_elegans" "106" "106.1"
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@ -1,10 +1,10 @@
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# You can use this file to create a conda environment for this module:
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# conda env create -f environment.yml
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name: nf-core-vep-105.0
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name: nf-core-vep-106.1
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- bioconda::ensembl-vep=105.0
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- bioconda::ensembl-vep=106.1
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@ -2,10 +2,10 @@ process ENSEMBLVEP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ensembl-vep=105.0" : null)
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conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' :
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'quay.io/biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }"
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'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' :
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'quay.io/biocontainers/ensembl-vep:106.1--pl5321h4a94de4_0' }"
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input:
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tuple val(meta), path(vcf)
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@ -16,7 +16,7 @@ workflow test_ensemblvep_fasta_json {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_tab {
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@ -27,7 +27,7 @@ workflow test_ensemblvep_fasta_tab {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta_vcf {
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@ -38,7 +38,7 @@ workflow test_ensemblvep_fasta_vcf {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_fasta {
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@ -49,7 +49,7 @@ workflow test_ensemblvep_fasta {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] )
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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
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}
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workflow test_ensemblvep_no_fasta {
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@ -58,5 +58,5 @@ workflow test_ensemblvep_no_fasta {
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] )
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ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], [], [] )
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}
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@ -3,21 +3,21 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: ENSEMBLVEP {
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container = 'nfcore/vep:104.3.WBcel235'
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container = 'nfcore/vep:106.1.WBcel235'
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}
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withName: ENSEMBLVEP_JSON {
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container = 'nfcore/vep:104.3.WBcel235'
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container = 'nfcore/vep:106.1.WBcel235'
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ext.args = '--json'
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}
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withName: ENSEMBLVEP_TAB {
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container = 'nfcore/vep:104.3.WBcel235'
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container = 'nfcore/vep:106.1.WBcel235'
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ext.args = '--tab'
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}
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withName: ENSEMBLVEP_VCF {
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container = 'nfcore/vep:104.3.WBcel235'
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container = 'nfcore/vep:106.1.WBcel235'
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ext.args = '--vcf'
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}
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}
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