diff --git a/CHANGELOG.md b/CHANGELOG.md index b2a249819a..d029450a20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#620](https://github.com/nf-core/sarek/pull/620) - Added checks for sex information when running a CNV tools - [#623](https://github.com/nf-core/sarek/pull/623) - Additional checks of data in the input sample sheet. - [#629](https://github.com/nf-core/sarek/pull/629) - Added checks to catch inconsistency between supplied samples and requested tools. +- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--snpeff_version` to allow more configuration on the snpeff container definition +- [#632](https://github.com/nf-core/sarek/pull/632) - Added params `--vep_include_fasta` to use the fasta file for annotation ### Changed @@ -81,6 +83,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta - [#620](https://github.com/nf-core/sarek/pull/620) - `gender` is now `sex` in the samplesheet - [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file +- [#632](https://github.com/nf-core/sarek/pull/632) - Update `snpEff` version to `5.1` and cache up to `105` +- [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106` ### Fixed diff --git a/conf/igenomes.config b/conf/igenomes.config index 9273c9090b..f3e5ece2c0 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -30,12 +30,13 @@ params { known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" known_indels_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem" - snpeff_db = 'GRCh37.75' + snpeff_db = 'GRCh37.87' snpeff_genome = 'GRCh37' - vep_cache_version = 105 + snpeff_version = '5.1' + vep_cache_version = 106 vep_genome = 'GRCh37' vep_species = 'homo_sapiens' - vep_version = '104.3' + vep_version = '106.1' } 'GATK.GRCh38' { ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip" @@ -60,21 +61,36 @@ params { mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem" pon = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz" pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi" - snpeff_db = 'GRCh38.99' + snpeff_db = 'GRCh38.105' snpeff_genome = 'GRCh38' - vep_cache_version = 105 + snpeff_version = '5.1' + vep_cache_version = 106 vep_genome = 'GRCh38' vep_species = 'homo_sapiens' - vep_version = '104.3' + vep_version = '106.1' } 'Ensembl.GRCh37' { bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" + snpeff_db = 'GRCh37.87' + snpeff_genome = 'GRCh37' + snpeff_version = '5.1' + vep_cache_version = 106 + vep_genome = 'GRCh37' + vep_species = 'homo_sapiens' + vep_version = '106.1' } 'NCBI.GRCh38' { bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + snpeff_db = 'GRCh38.105' + snpeff_genome = 'GRCh38' + snpeff_version = '5.1' + vep_cache_version = 106 + vep_genome = 'GRCh38' + vep_species = 'homo_sapiens' + vep_version = '106.1' } 'GRCm38' { bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" @@ -91,10 +107,11 @@ params { readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" snpeff_db = 'GRCm38.99' snpeff_genome = 'GRCm38' + snpeff_version = '5.1' vep_cache_version = 102 vep_genome = 'GRCm38' vep_species = 'mus_musculus' - vep_version = '104.3' + vep_version = '106.1' } 'TAIR10' { bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" @@ -114,17 +131,25 @@ params { 'WBcel235' { bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - snpeff_db = 'WBcel235.99' + snpeff_db = 'WBcel235.105' snpeff_genome = 'WBcel235' - vep_cache_version = 105 + snpeff_version = '5.1' + vep_cache_version = 106 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' - vep_version = '104.3' + vep_version = '106.1' } 'CanFam3.1' { bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" + snpeff_db = 'CanFam3.1.99' + snpeff_genome = 'CanFam3.1' + snpeff_version = '5.1' + vep_cache_version = 104 + vep_genome = 'CanFam3.1' + vep_species = 'canis_lupus_familiaris' + vep_version = '106.1' } 'GRCz10' { bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/modules.config b/conf/modules.config index f2feb006d4..b974befd77 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1133,7 +1133,7 @@ process{ withName: 'SNPEFF' { ext.prefix = { "${vcf.baseName.minus(".vcf")}_snpEff" } ext.args = '-nodownload -canon -v' - if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:5.0.${params.snpeff_genome}" : "nfcore/snpeff:5.0.${params.genome}" } + if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "nfcore/snpeff:${params.snpeff_version}.${params.genome}" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/reports/SnpEff/${meta.id}/${meta.variantcaller}" }, diff --git a/conf/test.config b/conf/test.config index f2cd22c0c6..dda176d7e9 100644 --- a/conf/test.config +++ b/conf/test.config @@ -36,12 +36,13 @@ params { germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'] intervals = params.test_data['homo_sapiens']['genome']['genome_interval_list'] known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'] - snpeff_db = 'WBcel235.99' + snpeff_db = 'WBcel235.105' snpeff_genome = 'WBcel235' - vep_cache_version = 104 + snpeff_version = '5.1' + vep_cache_version = 106 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' - vep_version = '104.3' + vep_version = '106.1' // Ignore params that will throw warning through params validation schema_ignore_params = "genomes,test_data" diff --git a/main.nf b/main.nf index 445e7d66ad..8bdfb18d76 100644 --- a/main.nf +++ b/main.nf @@ -51,10 +51,11 @@ params.pon = WorkflowMain.getGenomeAttribute(params, 'pon') params.pon_tbi = WorkflowMain.getGenomeAttribute(params, 'pon_tbi') params.snpeff_db = WorkflowMain.getGenomeAttribute(params, 'snpeff_db') params.snpeff_genome = WorkflowMain.getGenomeAttribute(params, 'snpeff_genome') +params.snpeff_version = WorkflowMain.getGenomeAttribute(params, 'snpeff_version') params.vep_cache_version = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version') -params.vep_version = WorkflowMain.getGenomeAttribute(params, 'vep_version') params.vep_genome = WorkflowMain.getGenomeAttribute(params, 'vep_genome') params.vep_species = WorkflowMain.getGenomeAttribute(params, 'vep_species') +params.vep_version = WorkflowMain.getGenomeAttribute(params, 'vep_version') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/modules.json b/modules.json index 9558720b38..16c1a8b54e 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "ensemblvep": { - "git_sha": "757c20c8ebfab85e1de9f98773a2269f6d34025a" + "git_sha": "973151e9eab9bac400aa99f099075a10cdd8e84c" }, "fastp": { "git_sha": "9b51362a532a14665f513cf987531f9ea5046b74" @@ -214,7 +214,7 @@ "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce" }, "snpeff": { - "git_sha": "40dd662fd26c3eb3160b7c8cbbe9bff80bbe2c30" + "git_sha": "d8bef6057bc2cf657d33ed496426be8416edd780" }, "strelka/germline": { "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" diff --git a/modules/nf-core/modules/ensemblvep/Dockerfile b/modules/nf-core/modules/ensemblvep/Dockerfile index 4ada7c6bbb..7d2c99c464 100644 --- a/modules/nf-core/modules/ensemblvep/Dockerfile +++ b/modules/nf-core/modules/ensemblvep/Dockerfile @@ -11,11 +11,11 @@ RUN conda env create -f /environment.yml && conda clean -a # Setup default ARG variables ARG GENOME=GRCh38 ARG SPECIES=homo_sapiens -ARG VEP_VERSION=105 -ARG VEP_TAG=105.0 +ARG VEP_CACHE_VERSION=106 +ARG VEP_VERSION=106.1 # 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 RUN vep_install \ @@ -23,9 +23,9 @@ RUN vep_install \ -c .vep \ -s ${SPECIES} \ -y ${GENOME} \ - --CACHE_VERSION ${VEP_VERSION} \ + --CACHE_VERSION ${VEP_CACHE_VERSION} \ --CONVERT \ --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml +RUN conda env export --name nf-core-vep-${VEP_VERSION} > nf-core-vep-${VEP_VERSION}.yml diff --git a/modules/nf-core/modules/ensemblvep/build.sh b/modules/nf-core/modules/ensemblvep/build.sh index 6f340c0f3d..eaa3ed5b4b 100644 --- a/modules/nf-core/modules/ensemblvep/build.sh +++ b/modules/nf-core/modules/ensemblvep/build.sh @@ -6,23 +6,23 @@ set -euo pipefail build_push() { GENOME=$1 SPECIES=$2 - VEP_VERSION=$3 - VEP_TAG=$4 + VEP_CACHE_VERSION=$3 + VEP_VERSION=$4 docker build \ . \ - -t nfcore/vep:${VEP_TAG}.${GENOME} \ + -t nfcore/vep:${VEP_VERSION}.${GENOME} \ --build-arg GENOME=${GENOME} \ --build-arg SPECIES=${SPECIES} \ - --build-arg VEP_VERSION=${VEP_VERSION} \ - --build-arg VEP_TAG=${VEP_TAG} + --build-arg VEP_CACHE_VERSION=${VEP_CACHE_VERSION} \ + --build-arg VEP_VERSION=${VEP_VERSION} - docker push nfcore/vep:${VEP_TAG}.${GENOME} + docker push nfcore/vep:${VEP_VERSION}.${GENOME} } -build_push "GRCh37" "homo_sapiens" "105" "105.0" -build_push "GRCh38" "homo_sapiens" "105" "105.0" -build_push "GRCm38" "mus_musculus" "102" "105.0" -build_push "GRCm39" "mus_musculus" "105" "105.0" -build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0" -build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" +build_push "GRCh37" "homo_sapiens" "106" "106.1" +build_push "GRCh38" "homo_sapiens" "106" "106.1" +build_push "GRCm38" "mus_musculus" "102" "106.1" +build_push "GRCm39" "mus_musculus" "106" "106.1" +build_push "CanFam3.1" "canis_lupus_familiaris" "104" "106.1" +build_push "WBcel235" "caenorhabditis_elegans" "106" "106.1" diff --git a/modules/nf-core/modules/ensemblvep/environment.yml b/modules/nf-core/modules/ensemblvep/environment.yml index 5df85b805d..d378f81061 100644 --- a/modules/nf-core/modules/ensemblvep/environment.yml +++ b/modules/nf-core/modules/ensemblvep/environment.yml @@ -1,10 +1,10 @@ # You can use this file to create a conda environment for this module: # conda env create -f environment.yml -name: nf-core-vep-105.0 +name: nf-core-vep-106.1 channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::ensembl-vep=105.0 + - bioconda::ensembl-vep=106.1 diff --git a/modules/nf-core/modules/ensemblvep/main.nf b/modules/nf-core/modules/ensemblvep/main.nf index d9bd3e831f..8a2c6363e9 100644 --- a/modules/nf-core/modules/ensemblvep/main.nf +++ b/modules/nf-core/modules/ensemblvep/main.nf @@ -2,10 +2,10 @@ process ENSEMBLVEP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::ensembl-vep=105.0" : null) + conda (params.enable_conda ? "bioconda::ensembl-vep=106.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : - 'quay.io/biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:106.1--pl5321h4a94de4_0' : + 'quay.io/biocontainers/ensembl-vep:106.1--pl5321h4a94de4_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/modules/snpeff/Dockerfile b/modules/nf-core/modules/snpeff/Dockerfile index d0e347573c..d3530de08e 100644 --- a/modules/nf-core/modules/snpeff/Dockerfile +++ b/modules/nf-core/modules/snpeff/Dockerfile @@ -1,4 +1,4 @@ -FROM nfcore/base:1.14 +FROM nfcore/base:2.1 LABEL \ author="Maxime Garcia" \ description="snpEff image for nf-core pipelines" \ @@ -11,13 +11,13 @@ RUN conda env create -f /environment.yml && conda clean -a # Setup default ARG variables ARG GENOME=GRCh38 ARG SNPEFF_CACHE_VERSION=99 -ARG SNPEFF_TAG=99 +ARG SNPEFF_VERSION=99 # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-snpeff-${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 diff --git a/modules/nf-core/modules/snpeff/build.sh b/modules/nf-core/modules/snpeff/build.sh index 2fccf9a8b4..4dcd6aa84a 100644 --- a/modules/nf-core/modules/snpeff/build.sh +++ b/modules/nf-core/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}.${GENOME} } -build_push "GRCh37" "75" "5.0" -build_push "GRCh38" "99" "5.0" -build_push "GRCm38" "99" "5.0" -build_push "CanFam3.1" "99" "5.0" -build_push "WBcel235" "99" "5.0" +build_push "GRCh37" "87" "5.1" +build_push "GRCh38" "105" "5.1" +build_push "GRCm38" "99" "5.1" +build_push "GRCm39" "105" "5.1" +build_push "CanFam3.1" "99" "5.1" +build_push "WBcel235" "105" "5.1" diff --git a/modules/nf-core/modules/snpeff/environment.yml b/modules/nf-core/modules/snpeff/environment.yml index ad0523fbd3..e0527690a6 100644 --- a/modules/nf-core/modules/snpeff/environment.yml +++ b/modules/nf-core/modules/snpeff/environment.yml @@ -1,10 +1,10 @@ # You can use this file to create a conda environment for this module: # conda env create -f environment.yml -name: nf-core-snpeff-5.0 +name: nf-core-snpeff-5.1 channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::snpeff=5.0 + - bioconda::snpeff=5.1 diff --git a/modules/nf-core/modules/snpeff/main.nf b/modules/nf-core/modules/snpeff/main.nf index 1b4d5f4309..e7743cac4c 100644 --- a/modules/nf-core/modules/snpeff/main.nf +++ b/modules/nf-core/modules/snpeff/main.nf @@ -2,10 +2,10 @@ process SNPEFF { tag "$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) diff --git a/nextflow.config b/nextflow.config index ea94858fb8..271c849648 100644 --- a/nextflow.config +++ b/nextflow.config @@ -88,6 +88,7 @@ params { annotation_cache = false // Annotation cache disabled snpeff_cache = null // No directory for snpEff cache vep_cache = null // No directory for VEP cache + vep_include_fasta = false // Don't use fasta file for annotation with VEP // MultiQC options multiqc_config = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 4c1b841bb2..1b10439d51 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -315,6 +315,13 @@ "default": "", "fa_icon": "fas fa-toolbox", "properties": { + "vep_include_fasta": { + "type": "boolean", + "fa_icon": "fas fa-database", + "description": "Allow usage of fasta file for annotation with VEP.\ncf https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta", + "default": false, + "hidden": true + }, "vep_dbnsfp": { "type": "boolean", "fa_icon": "fas fa-database", @@ -585,37 +592,44 @@ "snpeff_db": { "type": "string", "fa_icon": "fas fa-database", - "description": "snpEff DB version." + "description": "snpEff DB version.", + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the database to be use to annotate with.\nAlternatively databases' names can be listed with the `snpEff databases`." }, "snpeff_genome": { "type": "string", "fa_icon": "fas fa-microscope", - "description": "snpeff genome.", - "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." + "description": "snpEff genome.", + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the genome when using the container with pre-downloaded cache." + }, + "snpeff_version": { + "type": "string", + "fa_icon": "fas fa-tag", + "description": "snpEff version.", + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the snpeff version when using the container with pre-downloaded cache." }, "vep_genome": { "type": "string", "fa_icon": "fas fa-microscope", "description": "VEP genome.", - "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the genome when using the container with pre-downloaded cache." }, "vep_species": { "type": "string", "fa_icon": "fas fa-microscope", "description": "VEP species.", - "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively species listed in Ensembl Genomes caches can be used." }, "vep_cache_version": { "type": "number", "fa_icon": "fas fa-tag", "description": "VEP cache version.", - "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively cache version can be use to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers" }, "vep_version": { "type": "string", "fa_icon": "fas fa-tag", "description": "VEP version.", - "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the VEP version when using the container with pre-downloaded cache." }, "save_reference": { "type": "boolean", diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml index b98579dc44..1d82d63bac 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation.yml @@ -27,3 +27,12 @@ files: - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz.tbi +- name: Run VEP with fasta + command: nextflow run main.nf -profile test,annotation,docker --tools vep --vep_include_fasta --skip_tools multiqc + tags: + - annotation + - vep + files: + - path: results/annotation/test/test_VEP.ann.vcf.gz + - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi + - path: results/reports/EnsemblVEP/test/test_VEP.summary.html diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 1b38654e69..271c9b88b0 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -934,8 +934,10 @@ workflow SAREK { if (params.tools.contains('merge') || params.tools.contains('snpeff') || params.tools.contains('vep')) { + vep_fasta = (params.vep_include_fasta) ? fasta : [] + ANNOTATE(vcf_to_annotate, - fasta, + vep_fasta, params.tools, snpeff_db, snpeff_cache,