nf-test for snpsites (#5284)

* nf-test for snpsites

* remove old pytest

* Delete modules/nf-core/snpsites/tests/nextflow.config

* Update modules/nf-core/snpsites/tests/main.nf.test

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* Update assert

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* renamed test

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* reverted the input

* updated input...again

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* fixed typo

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>

* Regenerate snapshot and fix linting

---------

Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

modules/nf-core/snpsites/main.nf

@@ -35,4 +35,16 @@ process SNPSITES {
         snpsites: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
     END_VERSIONS
     """
+    stub:
+    """
+    touch filtered_alignment.fas
+    touch constant.sites.txt
+    CONSTANT_SITES=\$(cat constant.sites.txt)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snpsites: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
+    END_VERSIONS
+    """
+
 }

modules/nf-core/snpsites/meta.yml

@@ -28,6 +28,10 @@ output:
       type: file
       description: Text file containing counts of constant sites
       pattern: "*.{sites.txt}"
+  - constant_sites_string:
+      type: integer
+      description: Value with the number of constant sites
+      pattern: "*.{sites.txt}"
 authors:
   - "@avantonder"
 maintainers:

modules/nf-core/snpsites/tests/main.nf.test

@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process SNPSITES"
+    script "../main.nf"
+    process "SNPSITES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "snpsites"
+
+    test("sarscov2 - all_sites_fas") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - all_sites_fas - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/snpsites/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "sarscov2 - all_sites_fas - stub": {
+        "content": [
+            {
+                "0": [
+                    "filtered_alignment.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "constant.sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "versions.yml:md5,af6942a02036a7ff2eadb6ecf344c619"
+                ],
+                "3": [
+                    ""
+                ],
+                "constant_sites": [
+                    "constant.sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "constant_sites_string": [
+                    ""
+                ],
+                "fasta": [
+                    "filtered_alignment.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,af6942a02036a7ff2eadb6ecf344c619"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T15:20:57.589176616"
+    },
+    "sarscov2 - all_sites_fas": {
+        "content": [
+            {
+                "0": [
+                    "filtered_alignment.fas:md5,f96c7513003e878e16fa9eac9fcda0f4"
+                ],
+                "1": [
+                    "constant.sites.txt:md5,8b9b226e3787f7baaefce07405af22c9"
+                ],
+                "2": [
+                    "versions.yml:md5,af6942a02036a7ff2eadb6ecf344c619"
+                ],
+                "3": [
+                    "8789,5363,5747,9456"
+                ],
+                "constant_sites": [
+                    "constant.sites.txt:md5,8b9b226e3787f7baaefce07405af22c9"
+                ],
+                "constant_sites_string": [
+                    "8789,5363,5747,9456"
+                ],
+                "fasta": [
+                    "filtered_alignment.fas:md5,f96c7513003e878e16fa9eac9fcda0f4"
+                ],
+                "versions": [
+                    "versions.yml:md5,af6942a02036a7ff2eadb6ecf344c619"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T15:15:41.760289537"
+    }
+}

modules/nf-core/snpsites/tests/tags.yml

@@ -0,0 +1,2 @@
+snpsites:
+  - "modules/nf-core/snpsites/**"

tests/config/pytest_modules.yml

@@ -1579,9 +1579,6 @@ snpsift/dbnsfp:
 snpsift/split:
   - modules/nf-core/snpsift/split/**
   - tests/modules/nf-core/snpsift/split/**
-snpsites:
-  - modules/nf-core/snpsites/**
-  - tests/modules/nf-core/snpsites/**
 somalier/ancestry:
   - modules/nf-core/somalier/ancestry/**
   - tests/modules/nf-core/somalier/ancestry/**