nf-test custom/sratoolsncbisettings (nf-core#3964)

* Add nf-test for custom/sratoolsncbisettings

* Add custom/sratoolsncbisettings to tags

* Update custom/sratoolsncbisettings nf-test

* Remove pytest

* Add tags

* Snap update

* nf-test custom/sratoolsncbisettings fix test

* User configurable tmpdir via environment variable TMPDIR

* add custom configuration file

* Add config

* Add workflow from original test

* Re-add old tests back

* Check stdout of process

* Update tests to user iterator

.github/modules.yml

@@ -1,6 +1,9 @@
 custom/dumpsoftwareversions:
   - modules/nf-core/custom/dumpsoftwareversions/**
 
+custom/sratoolsncbisettings:
+  - modules/nf-core/custom/sratoolsncbisettings/**
+
 fastqc:
   - modules/nf-core/fastqc/**
 

modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test

@@ -0,0 +1,112 @@
+nextflow_process {
+
+    name "Test Process CUSTOM_SRATOOLSNCBISETTINGS"
+    script "../main.nf"
+    process "CUSTOM_SRATOOLSNCBISETTINGS"
+    config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
+    tag "custom"
+    tag "custom/sratoolsncbisettings"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                file(params.settings_path).mkdirs()
+                def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
+                settings.copyTo(params.settings_file)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.versions
+            ).match()
+
+            with(process.out.ncbi_settings) {
+                assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') }
+                assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') }
+            }
+        }
+
+    }
+
+    test("Should fail") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                file(params.settings_path).mkdirs()
+                def settings = file(params.settings_file)
+                settings.text = '''
+                ## auto-generated configuration file - DO NOT EDIT ##
+                config/default = "false"
+                /repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+                /repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
+                /repository/user/ad/public/apps/file/volumes/flatAd = "."
+                /repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
+                /repository/user/ad/public/apps/sra/volumes/sraAd = "."
+                /repository/user/ad/public/apps/sraPileup/volumes/ad = "."
+                /repository/user/ad/public/apps/sraRealign/volumes/ad = "."
+                /repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
+                /repository/user/ad/public/root = "."
+                /repository/user/default-path = "/root/ncbi"
+                '''.stripIndent()
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert snapshot(
+                process.out.versions
+            ).match()
+            assert process.stdout.any { it.contains('Command error:') }
+            assert process.stdout.any { it.contains('missing the required entries') }
+            assert process.stdout.any { it.contains('/LIBS/GUID') }
+            assert process.stdout.any { it.contains('/libs/cloud/report_instance_identity') }
+        }
+
+    }
+
+    test("Should run with nonexisting") {
+
+        when {
+            params {
+                settings_path = '/tmp/.ncbi'
+                settings_file = "${params.settings_path}/user-settings.mkfg"
+            }
+
+            process {
+                """
+                def settings = file(params.settings_file)
+                settings.delete()
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.versions).match()
+
+            with(process.out.ncbi_settings) {
+                { assert path(get(0)).readLines().any { it.contains('/LIBS/GUID') } }
+                { assert path(get(0)).readLines().any { it.contains('/libs/cloud/report_instance_identity') } }
+            }
+        }
+
+    }
+
+}

modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap

@@ -0,0 +1,18 @@
+{
+    "Should run with nonexisting": {
+        "content": [
+            [
+                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
+            ]
+        ],
+        "timestamp": "2023-10-12T12:24:24.023849"
+    },
+    "Should run without failures": {
+        "content": [
+            [
+                "versions.yml:md5,fec13b593c3b42ddd38f2fc77df25b70"
+            ]
+        ],
+        "timestamp": "2023-10-12T10:40:51.717351"
+    }
+}

tests/modules/nf-core/custom/sratoolsncbisettings/nextflow_mount.config → modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config

@@ -6,12 +6,11 @@ env.NCBI_SETTINGS = params.settings_file
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: CUSTOM_SRATOOLSNCBISETTINGS {
         containerOptions = {
             (workflow.containerEngine == 'singularity') ?
             "-B ${params.settings_path}:${params.settings_path}" :
             "-v ${params.settings_path}:${params.settings_path}"
         }
     }
-}
+}

nf-test.config

@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
+    workDir System.getenv("TMPDIR") ?: "/var/tmp"
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/config/nf-test.config"

tests/config/pytest_modules.yml

@@ -906,10 +906,6 @@ custom/matrixfilter:
   - modules/nf-core/custom/matrixfilter/**
   - tests/modules/nf-core/custom/matrixfilter/**
 
-custom/sratoolsncbisettings:
-  - modules/nf-core/custom/sratoolsncbisettings/**
-  - tests/modules/nf-core/custom/sratoolsncbisettings/**
-
 custom/tabulartogseacls:
   - modules/nf-core/custom/tabulartogseacls/**
   - tests/modules/nf-core/custom/tabulartogseacls/**