Merge pull request #248 from maxulysse/test_data_pipeline_s3

use s3 path for pipeline test data
nf-core · Jan 12, 2024 · ea0a0a3 · ea0a0a3
2 parents ff52f36 + 84adb51
commit ea0a0a3
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Showing 4 changed files with 5 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #242](https://github.com/nf-core/fetchngs/pull/242) - Template update for nf-core/tools v2.11
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
+- [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
 
 ### Software dependencies
 

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + '/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + 'modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                 """
             }
         }

diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = file(params.pipelines_test_data_base + '/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
+                input[0] = file(params.pipelines_test_data_base + 'modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv', checkIfExists: true)
                 """
             }
         }

diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -3,7 +3,7 @@ params {
     modules_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/3e79d4b5fbed8c6ef7546d50696b343ab9a95fbe/'
 
     // Base directory for pipeline test data
-    pipelines_test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/'
+    pipelines_test_data_base = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 }
 
 // Impose sensible resource limits for testing
@@ -24,4 +24,4 @@ manifest {
 timeline { enabled = false }
 report   { enabled = false }
 trace    { enabled = false }
-dag      { enabled = false }
+dag      { enabled = false }
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,7 +16,7 @@ nextflow_process { @@
                 process {
                     """
-                    input[0] = file(params.pipelines_test_data_base + '/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                    input[0] = file(params.pipelines_test_data_base + 'modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
                     """
                 }
             }
@@ Expand Down @@