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update ensemblvep to 106.1 and cache to 106 (#1876)

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Maxime U. Garcia 2022-07-13 13:43:03 +02:00 committed by GitHub
parent b6ed584443
commit 973151e9ea
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6 changed files with 31 additions and 31 deletions
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10
modules/ensemblvep/Dockerfile
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@ -11,11 +11,11 @@ RUN conda env create -f /environment.yml && conda clean -a
# Setup default ARG variables # Setup default ARG variables
ARG GENOME=GRCh38 ARG GENOME=GRCh38
ARG SPECIES=homo_sapiens ARG SPECIES=homo_sapiens
ARG VEP_VERSION=105 ARG VEP_CACHE_VERSION=106
ARG VEP_TAG=105.0 ARG VEP_VERSION=106.1
# Add conda installation dir to PATH (instead of doing 'conda activate') # Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH ENV PATH /opt/conda/envs/nf-core-vep-${VEP_VERSION}/bin:$PATH
# Download Genome # Download Genome
RUN vep_install \ RUN vep_install \
@ -23,9 +23,9 @@ RUN vep_install \
-c .vep \ -c .vep \
-s ${SPECIES} \ -s ${SPECIES} \
-y ${GENOME} \ -y ${GENOME} \
--CACHE_VERSION ${VEP_VERSION} \ --CACHE_VERSION ${VEP_CACHE_VERSION} \
--CONVERT \ --CONVERT \
--NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
# Dump the details of the installed packages to a file for posterity # Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml RUN conda env export --name nf-core-vep-${VEP_VERSION} > nf-core-vep-${VEP_VERSION}.yml

24
modules/ensemblvep/build.sh
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@ -6,23 +6,23 @@ set -euo pipefail
build_push() { build_push() {
GENOME=$1 GENOME=$1
SPECIES=$2 SPECIES=$2
VEP_VERSION=$3 VEP_CACHE_VERSION=$3
VEP_TAG=$4 VEP_VERSION=$4
docker build \ docker build \
. \ . \
-t nfcore/vep:${VEP_TAG}.${GENOME} \ -t nfcore/vep:${VEP_VERSION}.${GENOME} \
--build-arg GENOME=${GENOME} \ --build-arg GENOME=${GENOME} \
--build-arg SPECIES=${SPECIES} \ --build-arg SPECIES=${SPECIES} \
--build-arg VEP_VERSION=${VEP_VERSION} \ --build-arg VEP_CACHE_VERSION=${VEP_CACHE_VERSION} \
--build-arg VEP_TAG=${VEP_TAG} --build-arg VEP_VERSION=${VEP_VERSION}
docker push nfcore/vep:${VEP_TAG}.${GENOME} docker push nfcore/vep:${VEP_VERSION}.${GENOME}
} }
build_push "GRCh37" "homo_sapiens" "105" "105.0" build_push "GRCh37" "homo_sapiens" "106" "106.1"
build_push "GRCh38" "homo_sapiens" "105" "105.0" build_push "GRCh38" "homo_sapiens" "106" "106.1"
build_push "GRCm38" "mus_musculus" "102" "105.0" build_push "GRCm38" "mus_musculus" "102" "106.1"
build_push "GRCm39" "mus_musculus" "105" "105.0" build_push "GRCm39" "mus_musculus" "106" "106.1"
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0" build_push "CanFam3.1" "canis_lupus_familiaris" "104" "106.1"
build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" build_push "WBcel235" "caenorhabditis_elegans" "106" "106.1"

4
modules/ensemblvep/environment.yml
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@ -1,10 +1,10 @@
# You can use this file to create a conda environment for this module: # You can use this file to create a conda environment for this module:
# conda env create -f environment.yml # conda env create -f environment.yml
name: nf-core-vep-105.0 name: nf-core-vep-106.1
channels: channels:
- conda-forge - conda-forge
- bioconda - bioconda
- defaults - defaults
dependencies: dependencies:
- bioconda::ensembl-vep=105.0 - bioconda::ensembl-vep=106.1

6
modules/ensemblvep/main.nf
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@ -2,10 +2,10 @@ process ENSEMBLVEP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::ensembl-vep=105.0" : null) conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' :
'quay.io/biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" 'quay.io/biocontainers/ensembl-vep:106.1--pl5321h4a94de4_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

10
tests/modules/ensemblvep/main.nf
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@ -16,7 +16,7 @@ workflow test_ensemblvep_fasta_json {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] ) ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
} }
workflow test_ensemblvep_fasta_tab { workflow test_ensemblvep_fasta_tab {
@ -27,7 +27,7 @@ workflow test_ensemblvep_fasta_tab {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] ) ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
} }
workflow test_ensemblvep_fasta_vcf { workflow test_ensemblvep_fasta_vcf {
@ -38,7 +38,7 @@ workflow test_ensemblvep_fasta_vcf {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] ) ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
} }
workflow test_ensemblvep_fasta { workflow test_ensemblvep_fasta {
@ -49,7 +49,7 @@ workflow test_ensemblvep_fasta {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], fasta, [] ) ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
} }
workflow test_ensemblvep_no_fasta { workflow test_ensemblvep_no_fasta {
@ -58,5 +58,5 @@ workflow test_ensemblvep_no_fasta {
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
] ]
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [], [] ) ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], [], [] )
} }

8
tests/modules/ensemblvep/nextflow.config
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@ -3,21 +3,21 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: ENSEMBLVEP { withName: ENSEMBLVEP {
container = 'nfcore/vep:104.3.WBcel235' container = 'nfcore/vep:106.1.WBcel235'
} }
withName: ENSEMBLVEP_JSON { withName: ENSEMBLVEP_JSON {
container = 'nfcore/vep:104.3.WBcel235' container = 'nfcore/vep:106.1.WBcel235'
ext.args = '--json' ext.args = '--json'
} }
withName: ENSEMBLVEP_TAB { withName: ENSEMBLVEP_TAB {
container = 'nfcore/vep:104.3.WBcel235' container = 'nfcore/vep:106.1.WBcel235'
ext.args = '--tab' ext.args = '--tab'
} }
withName: ENSEMBLVEP_VCF { withName: ENSEMBLVEP_VCF {
container = 'nfcore/vep:104.3.WBcel235' container = 'nfcore/vep:106.1.WBcel235'
ext.args = '--vcf' ext.args = '--vcf'
} }
} }