Merge pull request #296 from drpatelh/fixes

Remove params.outdir from tests where required and update snapshots

Author: drpatelh

CHANGELOG.md

@@ -21,6 +21,7 @@ Special thanks to the following for their contributions to the release:
 - [Alexander Blaessle](https://github.com/alexblaessle)
 - [Lukas Forer](https://github.com/lukfor)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
@@ -52,6 +53,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #290](https://github.com/nf-core/fetchngs/pull/290) - Remove mentions of deprecated Synapse functionality in pipeline
 - [PR #294](https://github.com/nf-core/fetchngs/pull/294) - Replace mermaid diagram with subway map
 - [PR #295](https://github.com/nf-core/fetchngs/pull/295) - Be less stringent with test expectations for CI
+- [PR #296](https://github.com/nf-core/fetchngs/pull/296) - Remove params.outdir from tests where required and update snapshots
 
 ### Software dependencies
 

modules.json

@@ -7,23 +7,23 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
                         "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"]
                     }
                 }
@@ -32,22 +32,22 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "3aa09ac8899d7735cb5bc004da0ef5f35f9a7901",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/local/aspera_cli/tests/main.nf.test

@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [

modules/local/aspera_cli/tests/main.nf.test.snap

@@ -66,6 +66,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-29T13:00:29.847293"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:00.601018"
     }
 }

modules/local/multiqc_mappings_config/tests/main.nf.test

@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)

modules/local/multiqc_mappings_config/tests/main.nf.test.snap

@@ -22,6 +22,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:18.132284"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:12.65888"
     }
 }

modules/local/sra_fastq_ftp/tests/main.nf.test

@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [

modules/local/sra_fastq_ftp/tests/main.nf.test.snap

@@ -66,6 +66,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-12-20T23:33:35.159073"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:51.301654"
     }
 }

modules/local/sra_ids_to_runinfo/tests/main.nf.test

@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = 'SRR13191702'

modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap

@@ -16,6 +16,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:56.721948"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:52:05.345153"
     }
 }