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

* update snpeff to 5.1 and cache up to 105

* update dm5checksum

modules/snpeff/Dockerfile

@@ -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

modules/snpeff/build.sh

@@ -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"

modules/snpeff/environment.yml

@@ -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

modules/snpeff/main.nf

@@ -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)

tests/modules/snpeff/main.nf

@@ -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", [] )
 }

tests/modules/snpeff/nextflow.config

@@ -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'
     }
 
 }

tests/modules/snpeff/test.yml

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