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Fix release test profile paths
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@fellen31
fellen31 committed Sep 20, 2024
1 parent f0abc01 commit 8d5a120
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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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`
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32 changes: 16 additions & 16 deletions conf/test.config
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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
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68 changes: 34 additions & 34 deletions tests/main.nf.test
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/nextflow.config
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Expand Up @@ -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'
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