nf-test: Migrate phispy tests to nf-test (nf-core#5292)

* nf-test: Migrate phispy tests

* chore: Remove pytest test for phispy

* style: Change name to lowercase and fix license

* refactor: Change to test data base path

Signed-off-by: jvfe <jvfecav@gmail.com>

* refactor: Use with instead of variables

Signed-off-by: jvfe <jvfecav@gmail.com>

* refactor: Wrap with statements in assertAll

Signed-off-by: jvfe <jvfecav@gmail.com>

* refactor: Check the snapshot of every output except gbk

Signed-off-by: jvfe <jvfecav@gmail.com>

* fix: Change biopython version in environment

Signed-off-by: jvfe <jvfecav@gmail.com>

---------

Signed-off-by: jvfe <jvfecav@gmail.com>

modules/nf-core/phispy/environment.yml

@@ -1,7 +1,8 @@
-name: PhiSpy
+name: phispy
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - bioconda::phispy=4.2.21
+  - conda-forge::biopython=1.81

modules/nf-core/phispy/meta.yml

@@ -1,6 +1,6 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: "PhiSpy"
+name: "phispy"
 description: Predict prophages in bacterial genomes
 keywords:
   - genomics
@@ -16,7 +16,7 @@ tools:
       documentation: "https://github.com/linsalrob/PhiSpy/blob/master/README.md"
       tool_dev_url: "https://github.com/linsalrob/PhiSpy/"
       doi: "10.1093/nar/gks406"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

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

@@ -0,0 +1,87 @@
+// nf-core modules test phispy
+nextflow_process {
+
+    name "Test Process PHISPY"
+    script "../main.nf"
+    process "PHISPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "phispy"
+
+    test("bacteroides_fragilis - gbff") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true )
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    with(process.out.log[0]) {
+                        assert path(get(1)).text.contains('NZ_CP069563.1')
+                        assert path(get(1)).text.contains('91')
+                        assert path(get(1)).text.contains('Kept')
+                    }
+                },
+                {
+                    with(process.out.coordinates[0]) {
+                        assert path(get(1)).text.contains('NZ_CP069563.1')
+                        assert path(get(1)).text.contains('pp1')
+                        assert path(get(1)).text.contains('Longest Repeat flanking phage and within 2000 bp')
+                    }
+                },
+                { assert path(process.out.gbk[0][1]).linesGzip.toString().contains('5150703 bp') },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+    test("bacteroides_fragilis - gbff - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz", checkIfExists: true )
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.gbk[0][1]).exists() },
+                { assert snapshot(
+                        process.out.coordinates,
+                        process.out.log,
+                        process.out.information,
+                        process.out.bacteria_fasta,
+                        process.out.bacteria_gbk,
+                        process.out.phage_fasta,
+                        process.out.phage_gbk,
+                        process.out.prophage_gff,
+                        process.out.prophage_tbl,
+                        process.out.prophage_tsv,
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+}

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

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

tests/config/pytest_modules.yml

@@ -1468,9 +1468,6 @@ peka:
 phantompeakqualtools:
   - modules/nf-core/phantompeakqualtools/**
   - tests/modules/nf-core/phantompeakqualtools/**
-phispy:
-  - modules/nf-core/phispy/**
-  - tests/modules/nf-core/phispy/**
 phyloflash:
   - modules/nf-core/phyloflash/**
   - tests/modules/nf-core/phyloflash/**