From 2ef853676a1ef965cd5483dd90733f8e02aa2be3 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Fri, 20 Sep 2024 14:48:13 +0200 Subject: [PATCH] Fix release test profile paths --- CHANGELOG.md | 6 ++ conf/test.config | 32 ++++----- nextflow.config | 2 +- nextflow_schema.json | 2 +- .../local/snv_annotation/tests/main.nf.test | 16 ++--- tests/main.nf.test | 68 +++++++++---------- tests/nextflow.config | 2 +- 7 files changed, 67 insertions(+), 61 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d8c9ca80..547dbbe9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v0.3.2 - [2024-09-20] + +### `Fixed` + +- [#396](https://github.com/genomic-medicine-sweden/nallo/pull/396) - Fixed the release test profile not working, by pinning the testdata used [#395](https://github.com/genomic-medicine-sweden/nallo/issues/395) + ## v0.3.1 - [2024-09-11] ### `Fixed` diff --git a/conf/test.config b/conf/test.config index 8cc9b923..a348f829 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,35 +22,35 @@ params { // Genome references - fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' - input = 'https://github.com/genomic-medicine-sweden/test-datasets/raw/2948776ddf24ea131f527aa1f2dc23a43bb7b952/testdata/samplesheet.csv' + fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' + input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv' - bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' + bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' // HiFiCNV - hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' + hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' + hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' + hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed' // Dipcall - par_regions = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' + par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed' // Repeats - trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' + trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed' + variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json' // SNV Annotation - vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' - vep_plugin_files = params.pipelines_testdata_base_path + 'nallo/reference/vep_plugin_files.csv' - snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' + vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' + vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' + snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' // Rank variants - reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' - score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' // Somalier - somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' + somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' parallel_snv = 2 // Create 2 parallel DeepVariant processes preset = "revio" diff --git a/nextflow.config b/nextflow.config index 60687daf..3551d731 100644 --- a/nextflow.config +++ b/nextflow.config @@ -79,7 +79,7 @@ params { hook_url = null help = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/' // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 8e83ba04..40f4005b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -545,7 +545,7 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/", + "default": "https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/", "hidden": true } } diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test b/subworkflows/local/snv_annotation/tests/main.nf.test index 6009d4c2..0d288ccb 100644 --- a/subworkflows/local/snv_annotation/tests/main.nf.test +++ b/subworkflows/local/snv_annotation/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { """ input[0] = [ [ id:'hg38' ], - file(params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true) ] """ } @@ -33,7 +33,7 @@ nextflow_workflow { """ input[0] = [ [ id: 'test', num_intervals:1 ], - file(params.pipelines_testdata_base_path + 'nallo/testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.fastq.gz', checkIfExists: true) ] input[1] = GUNZIP.out.gunzip input[2] = true @@ -51,7 +51,7 @@ nextflow_workflow { .join(MINIMAP2_ALIGN.out.index) .join(Channel.of([ [ id: 'test', num_intervals:1 ], - file(params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed', checkifexists: true) + file(params.pipelines_testdata_base_path + 'reference/test_data.bed', checkifexists: true) ])) input[1] = GUNZIP.out.gunzip input[2] = SAMTOOLS_FAIDX.out.fai @@ -70,7 +70,7 @@ nextflow_workflow { """ input[0] = [ [ id: 'vep_cache' ], - file(params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz', checkIfExists:true) + file(params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz', checkIfExists:true) ] """ } @@ -85,14 +85,14 @@ nextflow_workflow { """ input[0] = SHORT_VARIANT_CALLING.out.combined_bcf input[1] = [ - file(params.pipelines_testdata_base_path + 'nallo/reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true) ] input[2] = GUNZIP.out.gunzip input[3] = SAMTOOLS_FAIDX.out.fai input[4] = UNTAR.out.untar.map { meta, cache -> cache } input[5] = Channel.value('110') input[6] = [ - file(params.pipelines_testdata_base_path + 'nallo/reference/vep_plugin_files.csv', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true) ] input[7] = false input[8] = Channel.value([]) @@ -127,14 +127,14 @@ nextflow_workflow { """ input[0] = SHORT_VARIANT_CALLING.out.combined_bcf input[1] = [ - file(params.pipelines_testdata_base_path + 'nallo/reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/cadd.v1.6.hg38.test_data.zip', checkIfExists: true) ] input[2] = GUNZIP.out.gunzip input[3] = SAMTOOLS_FAIDX.out.fai input[4] = UNTAR.out.untar.map { meta, cache -> cache } input[5] = Channel.value('110') input[6] = [ - file(params.pipelines_testdata_base_path + 'nallo/reference/vep_plugin_files.csv', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv', checkIfExists: true) ] input[7] = false input[8] = Channel.value([]) diff --git a/tests/main.nf.test b/tests/main.nf.test index 7584d5ad..7a79b71f 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -11,24 +11,24 @@ nextflow_pipeline { when { params { // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/' // Test files - fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' - input = 'https://github.com/genomic-medicine-sweden/test-datasets/raw/e2266a34c14d1e0a9ef798de3cd81a76c9216fc1/testdata/samplesheet.csv' - bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' - par_regions = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' - vep_plugin_files = params.pipelines_testdata_base_path + 'nallo/reference/vep_plugin_files.csv' - snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' - reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' - score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' + input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv' + bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' + hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' + hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' + hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed' + par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed' + trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed' + variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json' + vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' + vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' + snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' + somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' + reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' // Parameters parallel_snv = 2 @@ -144,24 +144,24 @@ nextflow_pipeline { when { params { // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/' // Test files - fasta = params.pipelines_testdata_base_path + 'nallo/reference/hg38.test.fa.gz' - input = 'https://github.com/genomic-medicine-sweden/test-datasets/raw/e2266a34c14d1e0a9ef798de3cd81a76c9216fc1/testdata/samplesheet_multisample_bam.csv' - bed = params.pipelines_testdata_base_path + 'nallo/reference/test_data.bed' - hificnv_xy = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XY.bed' - hificnv_xx = params.pipelines_testdata_base_path + 'nallo/reference/expected_cn.hg38.XX.bed' - hificnv_exclude = params.pipelines_testdata_base_path + 'nallo/reference/empty.bed' - par_regions = params.pipelines_testdata_base_path + 'nallo/reference/hs38.PAR.bed' - trgt_repeats = params.pipelines_testdata_base_path + 'nallo/reference/pathogenic_repeats.hg38.bed' - variant_catalog = params.pipelines_testdata_base_path + 'nallo/reference/variant_catalog_grch38.json' - vep_cache = params.pipelines_testdata_base_path + 'nallo/reference/vep_cache_test_data.tar.gz' - vep_plugin_files = params.pipelines_testdata_base_path + 'nallo/reference/vep_plugin_files.csv' - snp_db = params.pipelines_testdata_base_path + 'nallo/testdata/snp_dbs.csv' - somalier_sites = params.pipelines_testdata_base_path + 'nallo/reference/somalier_sites.vcf.gz' - reduced_penetrance = params.pipelines_testdata_base_path + 'nallo/reference/reduced_penetrance.tsv' - score_config_snv = params.pipelines_testdata_base_path + 'nallo/reference/rank_model_snv.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'nallo/reference/variant_consequences_v2.txt' + fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' + input = params.pipelines_testdata_base_path + 'testdata/samplesheet_multisample_bam.csv' + bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' + hificnv_xy = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' + hificnv_xx = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' + hificnv_exclude = params.pipelines_testdata_base_path + 'reference/empty.bed' + par_regions = params.pipelines_testdata_base_path + 'reference/hs38.PAR.bed' + trgt_repeats = params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed' + variant_catalog = params.pipelines_testdata_base_path + 'reference/variant_catalog_grch38.json' + vep_cache = params.pipelines_testdata_base_path + 'reference/vep_cache_test_data.tar.gz' + vep_plugin_files = params.pipelines_testdata_base_path + 'reference/vep_plugin_files.csv' + snp_db = params.pipelines_testdata_base_path + 'testdata/snp_dbs.csv' + somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' + reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' + score_config_snv = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' + variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' // Parameters parallel_snv = 2 diff --git a/tests/nextflow.config b/tests/nextflow.config index 3c53747a..2aa3910c 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -3,7 +3,7 @@ params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' // Base directory for genomic-medicine-sweden/nallo test data - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/genomic-medicine-sweden/test-datasets/nallo-0.3.2/' max_cpus = 4 max_memory = '15.GB'