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update snpeff to 5.1 and cache up to 105 (#1877)
* update snpeff to 5.1 and cache up to 105 * update dm5checksum
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parent
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commit
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7 changed files with 22 additions and 21 deletions
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@ -1,4 +1,4 @@
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FROM nfcore/base:1.14
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FROM nfcore/base:2.1
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LABEL \
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author="Maxime Garcia" \
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description="snpEff image for nf-core pipelines" \
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@ -11,13 +11,13 @@ 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 SNPEFF_CACHE_VERSION=99
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ARG SNPEFF_TAG=99
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ARG SNPEFF_VERSION=99
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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-snpeff-${SNPEFF_TAG}/bin:$PATH
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ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_VERSION}/bin:$PATH
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# Download Genome
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RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
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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-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml
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RUN conda env export --name nf-core-snpeff-${SNPEFF_VERSION} > nf-core-snpeff-${SNPEFF_VERSION}.yml
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19
modules/snpeff/build.sh
Normal file → Executable file
19
modules/snpeff/build.sh
Normal file → Executable file
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@ -6,20 +6,21 @@ set -euo pipefail
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build_push() {
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GENOME=$1
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SNPEFF_CACHE_VERSION=$2
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SNPEFF_TAG=$3
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SNPEFF_VERSION=$3
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docker build \
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. \
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-t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \
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-t nfcore/snpeff:${SNPEFF_VERSION}.${GENOME} \
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--build-arg GENOME=${GENOME} \
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--build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} \
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--build-arg SNPEFF_TAG=${SNPEFF_TAG}
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--build-arg SNPEFF_VERSION=${SNPEFF_VERSION}
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docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME}
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docker push nfcore/snpeff:${SNPEFF_VERSION}.${GENOME}
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}
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build_push "GRCh37" "75" "5.0"
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build_push "GRCh38" "99" "5.0"
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build_push "GRCm38" "99" "5.0"
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build_push "CanFam3.1" "99" "5.0"
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build_push "WBcel235" "99" "5.0"
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build_push "GRCh37" "87" "5.1"
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build_push "GRCh38" "105" "5.1"
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build_push "GRCm38" "99" "5.1"
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build_push "GRCm39" "105" "5.1"
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build_push "CanFam3.1" "99" "5.1"
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build_push "WBcel235" "105" "5.1"
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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-snpeff-5.0
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name: nf-core-snpeff-5.1
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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::snpeff=5.0
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- bioconda::snpeff=5.1
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@ -2,10 +2,10 @@ process SNPEFF {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
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conda (params.enable_conda ? "bioconda::snpeff=5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
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'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
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'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' :
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'quay.io/biocontainers/snpeff:5.1--hdfd78af_2' }"
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input:
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tuple val(meta), path(vcf)
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@ -10,5 +10,5 @@ workflow test_snpeff {
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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SNPEFF ( input, "WBcel235.99", [] )
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SNPEFF ( input, "WBcel235.105", [] )
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}
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@ -3,7 +3,7 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: SNPEFF {
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container = 'nfcore/snpeff:5.0.WBcel235'
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container = 'nfcore/snpeff:5.1.WBcel235'
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}
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}
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@ -4,5 +4,5 @@
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- snpeff
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files:
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- path: output/snpeff/test.ann.vcf
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md5sum: 42db84cb186e33c6992f9306627201ac
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md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
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- path: output/snpeff/test.csv
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