Updated test data paths batch 13 (#6087)

* Updated test data paths batch 13 * Updated snaphot * Update modules/nf-core/deepbgc/pipeline/meta.yml * Update modules/nf-core/propr/propr/meta.yml * Update modules/nf-core/toulligqc/meta.yml * Removed maintainers line --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 3, 2024 · 34ac993 · 34ac993
1 parent 9837ac7
commit 34ac993
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Showing 15 changed files with 92 additions and 89 deletions.
diff --git a/modules/nf-core/bcftools/call/tests/main.nf.test b/modules/nf-core/bcftools/call/tests/main.nf.test
@@ -19,8 +19,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -50,8 +50,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -84,8 +84,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -118,8 +118,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -152,11 +152,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -184,8 +184,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -216,8 +216,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -246,8 +246,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -276,8 +276,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []

diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test
@@ -18,8 +18,8 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -47,11 +47,11 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -76,8 +76,8 @@ nextflow_process {
                 """
                 input[0] = [ 
                     [ id:'out' ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []

diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test
@@ -18,8 +18,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -49,8 +49,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -83,8 +83,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -117,8 +117,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -151,11 +151,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
-                input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
                 input[3] = []
                 """
             }
@@ -183,8 +183,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -215,8 +215,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -245,8 +245,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []
@@ -275,8 +275,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'out', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = []
                 input[2] = []

diff --git a/modules/nf-core/deepbgc/pipeline/meta.yml b/modules/nf-core/deepbgc/pipeline/meta.yml
@@ -27,6 +27,9 @@ input:
       type: file
       description: FASTA/GenBank/Pfam CSV file
       pattern: "*.{fasta,fa,fna,gbk,csv}"
+  - db:
+      type: directory
+      description: Database path
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/deepbgc/pipeline/tests/main.nf.test b/modules/nf-core/deepbgc/pipeline/tests/main.nf.test
@@ -26,7 +26,7 @@ nextflow_process {
                 """
                 input[0] =  Channel.fromList([
                     tuple([ id:'test_gbk', single_end:false ], // meta map
-                            file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true))
+                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true))
                 ])
                 """
             }