Merge pull request #2877 from adamrtalbot/2858_test_data_uses_paths

Test data uses paths instead of config map
nf-core · Jun 26, 2024 · 7f28d6f · 7f28d6f
2 parents edc9b41 + af2cf15
commit 7f28d6f
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Showing 3 changed files with 15 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -114,6 +114,8 @@
 - fix(collectfile): sort true for methods_description_mqc.yaml ([#2947](https://github.com/nf-core/tools/pull/2947))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.3 ([#2951](https://github.com/nf-core/tools/pull/2951))
 - Restructure CHANGELOG.md ([#2954](https://github.com/nf-core/tools/pull/2954))
+- fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
+- Test data uses paths instead of config map ([#2877](https://github.com/nf-core/tools/pull/2877))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

diff --git a/nf_core/module-template/tests/main.nf.test.j2 b/nf_core/module-template/tests/main.nf.test.j2
@@ -28,10 +28,10 @@ nextflow_process {
                 {% if has_meta %}
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                 ]
                 {%- else %}
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                 {%- endif %}
                 """
             }
@@ -60,10 +60,10 @@ nextflow_process {
                 {% if has_meta %}
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
-                    ]
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
                 {%- else %}
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
                 {%- endif %}
                 """
             }

diff --git a/nf_core/subworkflow-template/tests/main.nf.test.j2 b/nf_core/subworkflow-template/tests/main.nf.test.j2
@@ -22,12 +22,14 @@ nextflow_workflow {
             workflow {
                 """
                 // TODO nf-core: define inputs of the workflow here. Example:
-                input[0] = [ [ id:'test', single_end:false ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
-                        ]
-                input[1] = [ [ id:'genome' ],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-                        ]
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
                 """
             }
         }