Merge pull request #320 from nf-core/318-update-for-tes-compliance

318 update for tes compliance

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
 - [PR #316](https://github.com/nf-core/fetchngs/pull/316) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
+- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance
+- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Refactor workflow tests
 - [PR #323](https://github.com/nf-core/fetchngs/pull/323) - Template update for nf-core/tools v3.0.2
 
 ### Software dependencies
@@ -42,6 +44,7 @@ Special thanks to the following for their contributions to the release:
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
+- [Venkat Malladi](https://github.com/vsmalladi)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 

modules.json

@@ -18,7 +18,7 @@
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
+                        "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {

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

@@ -67,9 +67,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T11:52:00.601018"
+        "timestamp": "2024-09-17T09:16:31.501413"
     }
 }

modules/local/multiqc_mappings_config/main.nf

@@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     path csv
 
     output:
-    path "*yml"        , emit: yml
+    path "*config.yml" , emit: yml
     path "versions.yml", emit: versions
 
     script:

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

@@ -3,10 +3,7 @@
         "content": [
             {
                 "0": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
+                    "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
                 ],
                 "1": [
                     "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
@@ -15,17 +12,14 @@
                     "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
                 ],
                 "yml": [
-                    [
-                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
-                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
-                    ]
+                    "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T11:52:12.65888"
+        "timestamp": "2024-09-17T09:16:46.557614"
     }
 }

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

@@ -67,9 +67,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T11:51:51.301654"
+        "timestamp": "2024-09-17T09:16:57.715689"
     }
-}
+}

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

@@ -17,9 +17,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T11:52:05.345153"
+        "timestamp": "2024-09-17T09:17:11.040523"
     }
 }

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

@@ -17,9 +17,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T11:51:45.748227"
+        "timestamp": "2024-09-17T09:17:23.371547"
     }
 }

nextflow.config

@@ -248,7 +248,7 @@ validation {
 \033[0;35m  ${manifest.name} ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 

workflows/sra/tests/main.nf.test

@@ -15,6 +15,9 @@ nextflow_workflow {
     test("Parameters: default") {
 
         when {
+            params {
+                outdir = "$outputDir"
+            }
             workflow {
                 """
                 input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035")
@@ -23,29 +26,15 @@ nextflow_workflow {
         }
 
         then {
-            assert workflow.success
-
             assertAll(
-                {
-                    with(workflow.out.samplesheet) {
-                        assert path(get(0)).readLines().size() == 4
-                        assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"']
-                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                    }
-                },
-                {
-                    with(workflow.out.mappings) {
-                        assert path(get(0)).readLines().size() == 4
-                        assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"']
-                        assert path(get(0)).text.contains('Illumina HiSeq 2500')
-                    }
-                },
-                {
-                    with(workflow.out.sample_mappings) {
-                        assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768"
-                    }
-                }
+                { assert workflow.success},
+                { assert snapshot(
+                    file(workflow.out.samplesheet[0]).name,
+                    workflow.out.mappings,
+                    workflow.out.sample_mappings,
+                    workflow.out.sra_metadata,
+                    workflow.out.versions
+                ).match() }
             )
         }
     }