From bea3ca998816a7f812b1bbbcb27c3a9ffbac0706 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Tue, 7 Feb 2023 12:49:50 +0100 Subject: [PATCH] New ensemblvep/download module (#2847) * ensemblvep -> ensemblvep/vep + add ensemblvep/download * update tags * lint * fix subworkflow tag * update exclude matrix * proper stub --- .github/workflows/pytest-workflow.yml | 4 +- modules/nf-core/ensemblvep/download/main.nf | 45 +++++++++++++ modules/nf-core/ensemblvep/download/meta.yml | 41 ++++++++++++ modules/nf-core/ensemblvep/{ => vep}/main.nf | 2 +- modules/nf-core/ensemblvep/{ => vep}/meta.yml | 2 +- .../nf-core/vcf_annotate_ensemblvep/main.nf | 20 +++--- tests/config/pytest_modules.yml | 16 +++-- .../nf-core/ensemblvep/download/main.nf | 11 ++++ .../ensemblvep/download/nextflow.config | 9 +++ .../nf-core/ensemblvep/download/test.yml | 7 +++ tests/modules/nf-core/ensemblvep/test.yml | 56 ----------------- .../nf-core/ensemblvep/{ => vep}/main.nf | 43 +++++++------ .../ensemblvep/{ => vep}/nextflow.config | 12 ++-- tests/modules/nf-core/ensemblvep/vep/test.yml | 63 +++++++++++++++++++ .../vcf_annotate_ensemblvep/nextflow.config | 2 +- 15 files changed, 229 insertions(+), 104 deletions(-) create mode 100644 modules/nf-core/ensemblvep/download/main.nf create mode 100644 modules/nf-core/ensemblvep/download/meta.yml rename modules/nf-core/ensemblvep/{ => vep}/main.nf (98%) rename modules/nf-core/ensemblvep/{ => vep}/meta.yml (98%) create mode 100644 tests/modules/nf-core/ensemblvep/download/main.nf create mode 100644 tests/modules/nf-core/ensemblvep/download/nextflow.config create mode 100644 tests/modules/nf-core/ensemblvep/download/test.yml delete mode 100644 tests/modules/nf-core/ensemblvep/test.yml rename tests/modules/nf-core/ensemblvep/{ => vep}/main.nf (50%) rename tests/modules/nf-core/ensemblvep/{ => vep}/nextflow.config (73%) create mode 100644 tests/modules/nf-core/ensemblvep/vep/test.yml diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 7978286cb78..8d9be513a4e 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -54,7 +54,7 @@ jobs: - profile: "conda" tags: deepvariant - profile: "conda" - tags: ensemblvep + tags: ensemblvep/vep - profile: "conda" tags: fastk/fastk - profile: "conda" @@ -81,6 +81,8 @@ jobs: tags: merquryfk/merquryfk - profile: "conda" tags: merquryfk/ploidyplot + - profile: "conda" + tags: subworkflows/vcf_annotate_ensemblvep env: NXF_ANSI_LOG: false steps: diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf new file mode 100644 index 00000000000..782fd5eaffd --- /dev/null +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -0,0 +1,45 @@ +process ENSEMBLVEP_DOWNLOAD { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::ensembl-vep=108.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ensembl-vep:108.2--pl5321h4a94de4_0' : + 'quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }" + + input: + tuple val(meta), val(assembly), val(species), val(cache_version) + + output: + tuple val(meta), path("vep_cache"), emit: cache + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + vep_install \\ + --CACHEDIR vep_cache \\ + --SPECIES $species \\ + --ASSEMBLY $assembly \\ + --CACHE_VERSION $cache_version \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS + """ + + stub: + """ + mkdir vep_cache + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml new file mode 100644 index 00000000000..ae84937d3ce --- /dev/null +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -0,0 +1,41 @@ +name: ENSEMBLVEP_DOWNLOAD +description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. +keywords: + - annotation +tools: + - ensemblvep: + description: | + VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs + or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. + homepage: https://www.ensembl.org/info/docs/tools/vep/index.html + documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html + licence: ["Apache-2.0"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: value + description: | + Genome assembly + - species: + type: value + description: | + Specie + - cache_version: + type: value + description: | + cache version +output: + - cache: + type: file + description: cache + pattern: "*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@maxulysse" diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf similarity index 98% rename from modules/nf-core/ensemblvep/main.nf rename to modules/nf-core/ensemblvep/vep/main.nf index 02132ababf6..e9d25f3dfd3 100644 --- a/modules/nf-core/ensemblvep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,4 +1,4 @@ -process ENSEMBLVEP { +process ENSEMBLVEP_VEP { tag "$meta.id" label 'process_medium' diff --git a/modules/nf-core/ensemblvep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml similarity index 98% rename from modules/nf-core/ensemblvep/meta.yml rename to modules/nf-core/ensemblvep/vep/meta.yml index 3faa6fe74a0..3a4f8d1db8f 100644 --- a/modules/nf-core/ensemblvep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP +name: ENSEMBLVEP_VEP description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf index b8305145b2d..c632f5a86dc 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf @@ -2,8 +2,8 @@ // Run VEP to annotate VCF files // -include { ENSEMBLVEP } from '../../../modules/nf-core/ensemblvep/main' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' +include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow VCF_ANNOTATE_ENSEMBLVEP { take: @@ -18,19 +18,19 @@ workflow VCF_ANNOTATE_ENSEMBLVEP { main: ch_versions = Channel.empty() - ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, vep_extra_files) - TABIX_TABIX(ENSEMBLVEP.out.vcf) + ENSEMBLVEP_VEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, vep_extra_files) + TABIX_TABIX(ENSEMBLVEP_VEP.out.vcf) - ch_vcf_tbi = ENSEMBLVEP.out.vcf.join(TABIX_TABIX.out.tbi) + ch_vcf_tbi = ENSEMBLVEP_VEP.out.vcf.join(TABIX_TABIX.out.tbi) // Gather versions of all tools used - ch_versions = ch_versions.mix(ENSEMBLVEP.out.versions) + ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: vcf_tbi = ch_vcf_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - json = ENSEMBLVEP.out.json // channel: [ val(meta), json ] - tab = ENSEMBLVEP.out.tab // channel: [ val(meta), tab ] - reports = ENSEMBLVEP.out.report // path: *.html - versions = ch_versions // path: versions.yml + json = ENSEMBLVEP_VEP.out.json // channel: [ val(meta), json ] + tab = ENSEMBLVEP_VEP.out.tab // channel: [ val(meta), tab ] + reports = ENSEMBLVEP_VEP.out.report // channel: [ *.html ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 8f2411edc8d..760cc0b5a0b 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -931,9 +931,13 @@ endorspy: - modules/nf-core/endorspy/** - tests/modules/nf-core/endorspy/** -ensemblvep: - - modules/nf-core/ensemblvep/** - - tests/modules/nf-core/ensemblvep/** +ensemblvep/download: + - modules/nf-core/ensemblvep/download/** + - tests/modules/nf-core/ensemblvep/download/** + +ensemblvep/vep: + - modules/nf-core/ensemblvep/vep/** + - tests/modules/nf-core/ensemblvep/vep/** entrezdirect/esearch: - modules/nf-core/entrezdirect/esearch/** @@ -3059,9 +3063,9 @@ subworkflows/homer/groseq: - subworkflows/nf-core/homer/groseq/** - tests/subworkflows/nf-core/homer/groseq/** -subworkflows/vcf_annotate_ensembl_vep: - - subworkflows/nf-core/vcf_annotate_ensembl_vep/** - - tests/subworkflows/nf-core/vcf_annotate_ensembl_vep/** +subworkflows/vcf_annotate_ensemblvep: + - subworkflows/nf-core/vcf_annotate_ensemblvep/** + - tests/subworkflows/nf-core/vcf_annotate_ensemblvep/** subworkflows/vcf_annotate_snpeff: - subworkflows/nf-core/vcf_annotate_snpeff/** diff --git a/tests/modules/nf-core/ensemblvep/download/main.nf b/tests/modules/nf-core/ensemblvep/download/main.nf new file mode 100644 index 00000000000..8e1c8de8c80 --- /dev/null +++ b/tests/modules/nf-core/ensemblvep/download/main.nf @@ -0,0 +1,11 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { ENSEMBLVEP_DOWNLOAD } from '../../../../../modules/nf-core/ensemblvep/download/main.nf' + +workflow test_ensemblvep_download { + input = [[id:"test"], "WBcel235", "caenorhabditis_elegans", "108"] + + ENSEMBLVEP_DOWNLOAD(input) +} diff --git a/tests/modules/nf-core/ensemblvep/download/nextflow.config b/tests/modules/nf-core/ensemblvep/download/nextflow.config new file mode 100644 index 00000000000..28c8e007ff9 --- /dev/null +++ b/tests/modules/nf-core/ensemblvep/download/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + } + +} diff --git a/tests/modules/nf-core/ensemblvep/download/test.yml b/tests/modules/nf-core/ensemblvep/download/test.yml new file mode 100644 index 00000000000..3add0978d94 --- /dev/null +++ b/tests/modules/nf-core/ensemblvep/download/test.yml @@ -0,0 +1,7 @@ +- name: ensemblvep test_ensemblvep_download + command: nextflow run ./tests/modules/nf-core/ensemblvep/download -entry test_ensemblvep_download -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/download/nextflow.config + tags: + - ensemblvep + - ensemblvep/download + files: + - path: output/ensemblvep/vep_cache/caenorhabditis_elegans/108_WBcel235/ diff --git a/tests/modules/nf-core/ensemblvep/test.yml b/tests/modules/nf-core/ensemblvep/test.yml deleted file mode 100644 index 2ce9d78b100..00000000000 --- a/tests/modules/nf-core/ensemblvep/test.yml +++ /dev/null @@ -1,56 +0,0 @@ -- name: ensemblvep test_ensemblvep_fasta_json - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.json.gz - md5sum: 709872fc2910431b1e8b7074bfe38c67 - - path: output/ensemblvep/test.summary.html - -- name: ensemblvep test_ensemblvep_fasta_tab - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.tab.gz - -- name: ensemblvep test_ensemblvep_fasta_vcf - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.vcf.gz - -- name: ensemblvep test_ensemblvep_fasta_vcf_bgzip - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.vcf.gz - -- name: ensemblvep test_ensemblvep_fasta_vcf_gzip - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.vcf.gz - -- name: ensemblvep test_ensemblvep_fasta - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.vcf.gz - -- name: ensemblvep test_ensemblvep_no_fasta - command: nextflow run ./tests/modules/nf-core/ensemblvep -entry test_ensemblvep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/nextflow.config - tags: - - ensemblvep - files: - - path: output/ensemblvep/test.summary.html - - path: output/ensemblvep/test.vcf.gz diff --git a/tests/modules/nf-core/ensemblvep/main.nf b/tests/modules/nf-core/ensemblvep/vep/main.nf similarity index 50% rename from tests/modules/nf-core/ensemblvep/main.nf rename to tests/modules/nf-core/ensemblvep/vep/main.nf index 7a2145d3c0d..bd8bb08ca6b 100644 --- a/tests/modules/nf-core/ensemblvep/main.nf +++ b/tests/modules/nf-core/ensemblvep/vep/main.nf @@ -2,15 +2,14 @@ nextflow.enable.dsl = 2 -include { ENSEMBLVEP } from '../../../../modules/nf-core/ensemblvep/main.nf' - -include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../../modules/nf-core/ensemblvep/main.nf' -include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../../modules/nf-core/ensemblvep/main.nf' - -workflow test_ensemblvep_fasta_json { +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_DEFAULT } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_JSON } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_TAB } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_BGZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_GZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf' + +workflow test_ensemblvep_vep_fasta_json { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -18,10 +17,10 @@ workflow test_ensemblvep_fasta_json { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_fasta_tab { +workflow test_ensemblvep_vep_fasta_tab { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -29,10 +28,10 @@ workflow test_ensemblvep_fasta_tab { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_fasta_vcf { +workflow test_ensemblvep_vep_fasta_vcf { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -40,10 +39,10 @@ workflow test_ensemblvep_fasta_vcf { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_fasta_vcf_bgzip { +workflow test_ensemblvep_vep_fasta_vcf_bgzip { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -51,10 +50,10 @@ workflow test_ensemblvep_fasta_vcf_bgzip { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_fasta_vcf_gzip { +workflow test_ensemblvep_vep_fasta_vcf_gzip { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -62,10 +61,10 @@ workflow test_ensemblvep_fasta_vcf_gzip { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_fasta { +workflow test_ensemblvep_vep_fasta { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) @@ -73,14 +72,14 @@ workflow test_ensemblvep_fasta { fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) + ENSEMBLVEP_VEP_DEFAULT ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] ) } -workflow test_ensemblvep_no_fasta { +workflow test_ensemblvep_vep_no_fasta { input = [ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] - ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], [], [] ) + ENSEMBLVEP_VEP_DEFAULT ( input, "WBcel235", "caenorhabditis_elegans", "108", [], [], [] ) } diff --git a/tests/modules/nf-core/ensemblvep/nextflow.config b/tests/modules/nf-core/ensemblvep/vep/nextflow.config similarity index 73% rename from tests/modules/nf-core/ensemblvep/nextflow.config rename to tests/modules/nf-core/ensemblvep/vep/nextflow.config index de292ac39f3..2f98e509d03 100644 --- a/tests/modules/nf-core/ensemblvep/nextflow.config +++ b/tests/modules/nf-core/ensemblvep/vep/nextflow.config @@ -2,31 +2,31 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: ENSEMBLVEP { + withName: ENSEMBLVEP_VEP_DEFAULT { container = 'nfcore/vep:108.2.WBcel235' } - withName: ENSEMBLVEP_JSON { + withName: ENSEMBLVEP_VEP_JSON { container = 'nfcore/vep:108.2.WBcel235' ext.args = '--json' } - withName: ENSEMBLVEP_TAB { + withName: ENSEMBLVEP_VEP_TAB { container = 'nfcore/vep:108.2.WBcel235' ext.args = '--tab' } - withName: ENSEMBLVEP_VCF { + withName: ENSEMBLVEP_VEP_VCF { container = 'nfcore/vep:108.2.WBcel235' ext.args = '--vcf' } - withName: ENSEMBLVEP_VCF_BGZIP { + withName: ENSEMBLVEP_VEP_VCF_BGZIP { container = 'nfcore/vep:108.2.WBcel235' ext.args = '--vcf --compress_output bgzip' } - withName: ENSEMBLVEP_VCF_GZIP { + withName: ENSEMBLVEP_VEP_VCF_GZIP { container = 'nfcore/vep:108.2.WBcel235' ext.args = '--vcf --compress_output gzip' } diff --git a/tests/modules/nf-core/ensemblvep/vep/test.yml b/tests/modules/nf-core/ensemblvep/vep/test.yml new file mode 100644 index 00000000000..7d25468ef6a --- /dev/null +++ b/tests/modules/nf-core/ensemblvep/vep/test.yml @@ -0,0 +1,63 @@ +- name: ensemblvep test_ensemblvep_vep_fasta_json + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta_json -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.json.gz + md5sum: 709872fc2910431b1e8b7074bfe38c67 + - path: output/ensemblvep/test.summary.html + +- name: ensemblvep test_ensemblvep_vep_fasta_tab + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta_tab -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.tab.gz + +- name: ensemblvep test_ensemblvep_vep_fasta_vcf + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.vcf.gz + +- name: ensemblvep test_ensemblvep_vep_fasta_vcf_bgzip + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta_vcf_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.vcf.gz + +- name: ensemblvep test_ensemblvep_vep_fasta_vcf_gzip + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta_vcf_gzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.vcf.gz + +- name: ensemblvep test_ensemblvep_vep_fasta + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.vcf.gz + +- name: ensemblvep test_ensemblvep_vep_no_fasta + command: nextflow run ./tests/modules/nf-core/ensemblvep/vep -entry test_ensemblvep_vep_no_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ensemblvep/vep/nextflow.config + tags: + - ensemblvep + - ensemblvep/vep + files: + - path: output/ensemblvep/test.summary.html + - path: output/ensemblvep/test.vcf.gz diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep/nextflow.config index 01774569561..fbc1578e3a5 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep/nextflow.config +++ b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep/nextflow.config @@ -2,7 +2,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: ENSEMBLVEP { + withName: ENSEMBLVEP_VEP { container = 'nfcore/vep:108.2.WBcel235' }