Merge pull request #32 from CarsonJM/dev

Updated nf-core modules to fix nf-tests
nf-core · Feb 2, 2024 · 8ccb7a9 · 8ccb7a9
2 parents 0f5f931 + cad6184
commit 8ccb7a9
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Showing 13 changed files with 155 additions and 44 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,4 +7,5 @@ testing/
 testing*
 *.pyc
 .nf-tests/
+.nf-test/
 .nf-test.log
diff --git a/modules.json b/modules.json
@@ -33,12 +33,12 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
+                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
+                        "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
                         "installed_by": ["modules"]
                     },
                     "ncbigenomedownload": {
@@ -48,7 +48,7 @@
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -158,7 +158,7 @@
                 },
                 "target_capture_fshape": {
                     "type": "number",
-                    "default": 6,
+                    "default": 6.0,
                     "description": "Shape parameter of the fragment size distribution."
                 },
                 "target_capture_smedian": {
@@ -168,7 +168,7 @@
                 },
                 "target_capture_sshape": {
                     "type": "number",
-                    "default": 6,
+                    "default": 6.0,
                     "description": "Shape parameter of the fragment size distribution."
                 },
                 "target_capture_tmedian": {

diff --git a/nf-test.config b/nf-test.config
@@ -1,16 +1,10 @@
 config {
-    // location for all nf-tests
+    // Location of nf-tests
     testsDir "."
 
-    // nf-test directory including temporary files for each test
-    workDir ".nf-tests"
+    // nf-test directory used to create temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
-    // location of library folder that is added automatically to the classpath
-    libDir "lib/"
-
-    // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
-
-    // run all test with the defined docker profile from the main nextflow.config
-    profile ""
+    // Location of an optional nextflow.config file specific for executing pipeline tests
+    configFile "tests/nextflow.config"
 }
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -0,0 +1,27 @@
+params {
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
+}
+
+// Load test_data.config for for using test-datasets
+includeConfig '../conf/test_data.config'
+
+// Impose sensible resource limits for testing
+process {
+    withName: '.*' {
+        cpus   = 2
+        memory = 3.GB
+        time   = 2.h
+    }
+}
+
+// Impose same minimum Nextflow version as the pipeline for testing
+manifest {
+    nextflowVersion = '!>=23.04.0'
+}
+
+// Disable all Nextflow reporting options
+timeline { enabled = false }
+report   { enabled = false }
+trace    { enabled = false }
+dag      { enabled = false }