Merge pull request #396 from fellen31/patch

Patch release 0.3.2
genomic-medicine-sweden · Sep 23, 2024 · fd32ed6 · fd32ed6
2 parents f0abc01 + 2ef8536
commit fd32ed6
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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'