update snpeff to 5.1 and cache up to 105 (#1877)

* update snpeff to 5.1 and cache up to 105

* update dm5checksum
This commit is contained in:
Maxime U. Garcia 2022-07-13 15:16:21 +02:00 committed by GitHub
parent 973151e9ea
commit d8bef6057b
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 22 additions and 21 deletions

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@ -1,4 +1,4 @@
FROM nfcore/base:1.14
FROM nfcore/base:2.1
LABEL \
author="Maxime Garcia" \
description="snpEff image for nf-core pipelines" \
@ -11,13 +11,13 @@ RUN conda env create -f /environment.yml && conda clean -a
# Setup default ARG variables
ARG GENOME=GRCh38
ARG SNPEFF_CACHE_VERSION=99
ARG SNPEFF_TAG=99
ARG SNPEFF_VERSION=99
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_TAG}/bin:$PATH
ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_VERSION}/bin:$PATH
# Download Genome
RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml
RUN conda env export --name nf-core-snpeff-${SNPEFF_VERSION} > nf-core-snpeff-${SNPEFF_VERSION}.yml

19
modules/snpeff/build.sh Normal file → Executable file
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@ -6,20 +6,21 @@ set -euo pipefail
build_push() {
GENOME=$1
SNPEFF_CACHE_VERSION=$2
SNPEFF_TAG=$3
SNPEFF_VERSION=$3
docker build \
. \
-t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \
-t nfcore/snpeff:${SNPEFF_VERSION}.${GENOME} \
--build-arg GENOME=${GENOME} \
--build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} \
--build-arg SNPEFF_TAG=${SNPEFF_TAG}
--build-arg SNPEFF_VERSION=${SNPEFF_VERSION}
docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME}
docker push nfcore/snpeff:${SNPEFF_VERSION}.${GENOME}
}
build_push "GRCh37" "75" "5.0"
build_push "GRCh38" "99" "5.0"
build_push "GRCm38" "99" "5.0"
build_push "CanFam3.1" "99" "5.0"
build_push "WBcel235" "99" "5.0"
build_push "GRCh37" "87" "5.1"
build_push "GRCh38" "105" "5.1"
build_push "GRCm38" "99" "5.1"
build_push "GRCm39" "105" "5.1"
build_push "CanFam3.1" "99" "5.1"
build_push "WBcel235" "105" "5.1"

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@ -1,10 +1,10 @@
# You can use this file to create a conda environment for this module:
# conda env create -f environment.yml
name: nf-core-snpeff-5.0
name: nf-core-snpeff-5.1
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::snpeff=5.0
- bioconda::snpeff=5.1

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@ -2,10 +2,10 @@ process SNPEFF {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
conda (params.enable_conda ? "bioconda::snpeff=5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' :
'quay.io/biocontainers/snpeff:5.1--hdfd78af_2' }"
input:
tuple val(meta), path(vcf)

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@ -10,5 +10,5 @@ workflow test_snpeff {
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
]
SNPEFF ( input, "WBcel235.99", [] )
SNPEFF ( input, "WBcel235.105", [] )
}

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@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SNPEFF {
container = 'nfcore/snpeff:5.0.WBcel235'
container = 'nfcore/snpeff:5.1.WBcel235'
}
}

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@ -4,5 +4,5 @@
- snpeff
files:
- path: output/snpeff/test.ann.vcf
md5sum: 42db84cb186e33c6992f9306627201ac
md5sum: e933384e572fc5ed0cce0faf1c0b2cc9
- path: output/snpeff/test.csv