Merge pull request #296 from drpatelh/fixes

Remove params.outdir from tests where required and update snapshots
nf-core · Feb 29, 2024 · 03ac573 · 03ac573
2 parents 89e3716 + f6cf223
commit 03ac573
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diff --git a/CHANGELOG.md b/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
 

diff --git a/modules.json b/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"]
                     }
                 }

diff --git a/modules/local/aspera_cli/tests/main.nf.test b/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] = [

diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/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"
     }
 }
diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/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)

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/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"
     }
 }
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/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] = [

diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/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"
     }
 }
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/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'

diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/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"
     }
 }
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/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 + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true)

diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap
@@ -16,6 +16,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:36.16611"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:45.748227"
     }
 }
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -7,10 +7,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
-
             process {
                 """
                 input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867',  experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7',  sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false]

diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap
@@ -108,6 +108,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:27.169349"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T11:51:38.244046"
     }
 }
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config
diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test