From 4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 25 Jul 2023 16:06:46 +0200 Subject: [PATCH] Remove containers with cache with snpEff too (#3670) * update tests for snpeff * remove containers in config * fix cache version in tests * update meta.yml * fix meta.yml * fix meta data * fix md5sum * re-enable conda tests --- .github/workflows/pytest-workflow.yml | 2 -- modules/nf-core/snpeff/download/meta.yml | 6 +++++- modules/nf-core/snpeff/snpeff/main.nf | 2 +- modules/nf-core/snpeff/snpeff/meta.yml | 4 +++- tests/modules/nf-core/snpeff/download/main.nf | 8 +++++--- tests/modules/nf-core/snpeff/snpeff/main.nf | 17 +++++++++++++---- .../nf-core/snpeff/snpeff/nextflow.config | 4 ---- tests/modules/nf-core/snpeff/snpeff/test.yml | 2 +- .../vcf_annotate_ensemblvep_snpeff/main.nf | 18 ++++++++++++++---- .../nextflow.config | 4 ---- .../nf-core/vcf_annotate_snpeff/main.nf | 17 +++++++++++++---- .../vcf_annotate_snpeff/nextflow.config | 1 - 12 files changed, 55 insertions(+), 30 deletions(-) diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 251af103d4f..38dfba8c6da 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -146,8 +146,6 @@ jobs: tags: gatk4/determinegermlinecontigploidy - profile: "conda" tags: subworkflows/bcl_demultiplex - - profile: "conda" - tags: subworkflows/vcf_annotate_ensemblvep_snpeff - profile: "conda" tags: subworkflows/fasta_clean_fcs - profile: "conda" diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index 07a7afaf8bb..3c03c2f602e 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -2,6 +2,10 @@ name: SNPEFF_DOWNLOAD description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation + - effect prediction + - snpeff + - variant + - vcf tools: - snpeff: description: | @@ -21,7 +25,7 @@ input: description: | vcf to annotate - db: - type: value + type: string description: | which db to annotate with output: diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index 84f5ee5d58a..e92c1597e77 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -10,7 +10,7 @@ process SNPEFF_SNPEFF { input: tuple val(meta), path(vcf) val db - path cache + tuple val(meta2), path(cache) output: tuple val(meta), path("*.ann.vcf"), emit: vcf diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index cf00c819ac7..44bada2303c 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -2,8 +2,10 @@ name: SNPEFF_SNPEFF description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation - - variant - effect prediction + - snpeff + - variant + - vcf tools: - snpeff: description: | diff --git a/tests/modules/nf-core/snpeff/download/main.nf b/tests/modules/nf-core/snpeff/download/main.nf index b36a710d8e5..dfefff98749 100644 --- a/tests/modules/nf-core/snpeff/download/main.nf +++ b/tests/modules/nf-core/snpeff/download/main.nf @@ -4,8 +4,10 @@ nextflow.enable.dsl = 2 include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main.nf' -workflow test_snpeff_download { - input = [ [ id:'test' ], "WBcel235", "105"] +snpeff_cache_version = "105" +snpeff_genome = "WBcel235" +snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version]) - SNPEFF_DOWNLOAD ( input ) +workflow test_snpeff_download { + SNPEFF_DOWNLOAD(snpeff_cache_input) } diff --git a/tests/modules/nf-core/snpeff/snpeff/main.nf b/tests/modules/nf-core/snpeff/snpeff/main.nf index cf33abf233a..68150677abb 100644 --- a/tests/modules/nf-core/snpeff/snpeff/main.nf +++ b/tests/modules/nf-core/snpeff/snpeff/main.nf @@ -2,13 +2,22 @@ nextflow.enable.dsl = 2 -include { SNPEFF_SNPEFF } from '../../../../../modules/nf-core/snpeff/snpeff/main.nf' +include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main' +include { SNPEFF_SNPEFF } from '../../../../../modules/nf-core/snpeff/snpeff/main' + +snpeff_cache_version = "105" +snpeff_genome = "WBcel235" +snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version]) workflow test_snpeff_snpeff { - input = [ + input = Channel.of([ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) - ] + ]) + + SNPEFF_DOWNLOAD(snpeff_cache_input) + + snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() - SNPEFF_SNPEFF ( input, "WBcel235.105", [] ) + SNPEFF_SNPEFF(input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache) } diff --git a/tests/modules/nf-core/snpeff/snpeff/nextflow.config b/tests/modules/nf-core/snpeff/snpeff/nextflow.config index d761d06bef4..8730f1c4b93 100644 --- a/tests/modules/nf-core/snpeff/snpeff/nextflow.config +++ b/tests/modules/nf-core/snpeff/snpeff/nextflow.config @@ -2,8 +2,4 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: SNPEFF_SNPEFF { - container = 'docker.io/nfcore/snpeff:5.1.WBcel235' - } - } diff --git a/tests/modules/nf-core/snpeff/snpeff/test.yml b/tests/modules/nf-core/snpeff/snpeff/test.yml index 0c0df7fab3b..62d3b78dc7a 100644 --- a/tests/modules/nf-core/snpeff/snpeff/test.yml +++ b/tests/modules/nf-core/snpeff/snpeff/test.yml @@ -5,7 +5,7 @@ - snpeff/snpeff files: - path: output/snpeff/test.ann.vcf - md5sum: e933384e572fc5ed0cce0faf1c0b2cc9 + md5sum: 9dc12cf54c78516abf3558672d3746d0 - path: output/snpeff/test.csv - path: output/snpeff/test.genes.txt md5sum: 130536bf0237d7f3f746d32aaa32840a diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf index 0d44a919ee0..ce160e4756b 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf +++ b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf @@ -3,8 +3,12 @@ nextflow.enable.dsl = 2 include { ENSEMBLVEP_DOWNLOAD } from '../../../../modules/nf-core/ensemblvep/download/main' +include { SNPEFF_DOWNLOAD } from '../../../../modules/nf-core/snpeff/download/main' include { VCF_ANNOTATE_ENSEMBLVEP_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main' +snpeff_cache_version = "105" +snpeff_genome = "WBcel235" +snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version]) vep_cache_version = "110" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" @@ -61,6 +65,10 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff { ] ]) + SNPEFF_DOWNLOAD(snpeff_cache_input) + + snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() + VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( input, [[],[]], @@ -69,8 +77,8 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff { [], [], [], - "WBcel235.99", - [], + "${snpeff_genome}.${snpeff_cache_version}", + snpeff_cache, ["snpeff"], 5 ) @@ -93,7 +101,9 @@ workflow vcf_annotate_ensemblvep_snpeff_both { ]) ENSEMBLVEP_DOWNLOAD(vep_cache_input) + SNPEFF_DOWNLOAD(snpeff_cache_input) + snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first() VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( @@ -104,8 +114,8 @@ workflow vcf_annotate_ensemblvep_snpeff_both { vep_cache_version, vep_cache, [], - "WBcel235.99", - [], + "${snpeff_genome}.${snpeff_cache_version}", + snpeff_cache, ["ensemblvep", "snpeff"], 5 ) diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config index 8a584f0b3d1..fa4f5b43091 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config +++ b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config @@ -17,8 +17,4 @@ process { ].join(" ")} } - withName: SNPEFF_SNPEFF { - container = 'docker.io/nfcore/snpeff:5.0.WBcel235' - } - } diff --git a/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf index 1db1ffcf36b..d2451765c7a 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf +++ b/tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf @@ -2,13 +2,22 @@ nextflow.enable.dsl = 2 -include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main.nf' +include { SNPEFF_DOWNLOAD } from '../../../../modules/nf-core/snpeff/download/main' +include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main' + +snpeff_cache_version = "105" +snpeff_genome = "WBcel235" +snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version]) workflow vcf_annotate_snpeff { - input = [ + input = Channel.of([ [ id:'test' ], // meta map file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) - ] + ]) + + SNPEFF_DOWNLOAD(snpeff_cache_input) + + snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() - VCF_ANNOTATE_SNPEFF ( input, "WBcel235.99", [] ) + VCF_ANNOTATE_SNPEFF ( input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache ) } diff --git a/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config index 3edd9d068ed..de8c0e98231 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config +++ b/tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config @@ -3,7 +3,6 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SNPEFF_SNPEFF { - container = 'docker.io/nfcore/snpeff:5.0.WBcel235' publishDir = [ path: { "output/snpeff/test/" }, pattern: "*{csv,html,genes.txt}"