Merge branch 'dev' into fix_rrnatranscript_bug

nf-core · Dec 3, 2024 · 9602378 · 9602378
2 parents 837507d + d742f87
commit 9602378
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Showing 6 changed files with 131 additions and 2 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
+          - "latest-stable"
         trim_parameters:
           - "--fastp_trim false"
           - "--fastp_trim true"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Option to avoid using COSMIC (for example in the case of clinical use) [547](https://github.com/nf-core/rnafusion/pull/547)
 - Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
 - Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554)
+- Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)
 
 ### Changed
 

diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf
@@ -6,7 +6,11 @@ process FUSIONREPORT_DOWNLOAD {
     container "docker.io/clinicalgenomics/fusion-report:3.1.0"
 
     output:
-    path "*"                , emit: reference
+    path "fusiongdb2.db"    , emit: fusiongdb2
+    path "mitelman.db"      , emit: mitelman
+    path "cosmic.db"        , emit: cosmic, optional: true
+    path "*.txt"            , emit: timestamp
+    path "*.log"            , emit: log
     path "versions.yml"     , emit: versions
 
     script:
@@ -26,6 +30,9 @@ process FUSIONREPORT_DOWNLOAD {
     touch cosmic.db
     touch fusiongdb2.db
     touch mitelman.db
+    touch DB-timestamp.txt
+    touch fusion_report.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fusion_report: \$(fusion_report --version | sed 's/fusion-report //')

diff --git a/modules/local/fusionreport/download/tests/main.nf.test b/modules/local/fusionreport/download/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process FUSIONREPORT_DOWNLOAD"
+    script "../main.nf"
+    process "FUSIONREPORT_DOWNLOAD"
+
+    test("Download fusionreport databases") {
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                // This process doesn't have any inputs
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fusiongdb2,
+                    process.out.mitelman,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Create stub files") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // This process doesn't have any inputs
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/local/fusionreport/download/tests/main.nf.test.snap b/modules/local/fusionreport/download/tests/main.nf.test.snap
@@ -0,0 +1,67 @@
+{
+    "Download fusionreport databases": {
+        "content": [
+            [
+                "fusiongdb2.db:md5,e1ac123a744e515d3e5f85b8344d526a"
+            ],
+            [
+                "mitelman.db:md5,1363795c97f77c641065ecd9ad0e484a"
+            ],
+            [
+                "versions.yml:md5,fa5f13c563f431912048c1802b5a0c74"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-02T13:09:56.930477745"
+    },
+    "Create stub files": {
+        "content": [
+            {
+                "0": [
+                    "fusiongdb2.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "mitelman.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "cosmic.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "3": [
+                    "DB-timestamp.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "4": [
+                    "fusion_report.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "versions.yml:md5,fa5f13c563f431912048c1802b5a0c74"
+                ],
+                "cosmic": [
+                    "cosmic.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "fusiongdb2": [
+                    "fusiongdb2.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "log": [
+                    "fusion_report.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "mitelman": [
+                    "mitelman.db:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "timestamp": [
+                    "DB-timestamp.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,fa5f13c563f431912048c1802b5a0c74"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-02T13:10:12.577952658"
+    }
+}
diff --git a/modules/local/fusionreport/download/tests/nextflow.config b/modules/local/fusionreport/download/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'FUSIONREPORT_DOWNLOAD' {
+        ext.args         =  "--no-cosmic"
+    }
+}