Added nf-test for pirate (#6560)

nf-core · Sep 5, 2024 · e942cbf · e942cbf
1 parent 8b74c80
commit e942cbf
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Showing 8 changed files with 175 additions and 126 deletions.
diff --git a/modules/nf-core/pirate/environment.yml b/modules/nf-core/pirate/environment.yml
@@ -1,8 +1,10 @@
 name: pirate
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::pirate=1.0.4
   - bioconda::perl-bioperl=1.7.2
+  - bioconda::pirate=1.0.4
diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf
@@ -33,4 +33,16 @@ process PIRATE {
         pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir results
+
+    touch results/PIRATE.gene_families.ordered.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/pirate/tests/main.nf.test b/modules/nf-core/pirate/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process PIRATE"
+    script "../main.nf"
+    process "PIRATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pirate"
+
+    test("test-pirate") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff', checkIfExists: true)
+				    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        process.out.results[0][1].collect { file(it).name },
+                        process.out.aln,
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-pirate-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff', checkIfExists: true)
+				    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/pirate/tests/main.nf.test.snap b/modules/nf-core/pirate/tests/main.nf.test.snap
@@ -0,0 +1,90 @@
+{
+    "test-pirate": {
+        "content": [
+            [
+                "PIRATE.gene_families.ordered.tsv",
+                "PIRATE.gene_families.tsv",
+                "PIRATE.genomes_per_allele.tsv",
+                "PIRATE.log",
+                "PIRATE.pangenome_summary.txt",
+                "PIRATE.unique_alleles.tsv",
+                "binary_presence_absence.fasta",
+                "binary_presence_absence.nwk",
+                "cluster_alleles.tab",
+                "co-ords",
+                "genome2loci.tab",
+                "genome_list.txt",
+                "link_clusters.log",
+                "loci_list.tab",
+                "loci_paralog_categories.tab",
+                "modified_gffs",
+                "pan_sequences.fasta",
+                "pangenome.connected_blocks.tsv",
+                "pangenome.edges",
+                "pangenome.gfa",
+                "pangenome.order.tsv",
+                "pangenome.reversed.tsv",
+                "pangenome.syntenic_blocks.tsv",
+                "pangenome.temp",
+                "pangenome_iterations",
+                "pangenome_log.txt",
+                "paralog_clusters.tab",
+                "representative_sequences.faa",
+                "representative_sequences.ffn",
+                "split_groups.log"
+            ],
+            [
+
+            ],
+            [
+                "versions.yml:md5,2f5a68c53da1146ee3000263ea61d769"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T16:38:56.92857"
+    },
+    "test-pirate-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "PIRATE.gene_families.ordered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,2f5a68c53da1146ee3000263ea61d769"
+                ],
+                "aln": [
+
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "PIRATE.gene_families.ordered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2f5a68c53da1146ee3000263ea61d769"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T16:18:13.292321"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -608,9 +608,6 @@ picard/collectrnaseqmetrics:
 picard/filtersamreads:
   - modules/nf-core/picard/filtersamreads/**
   - tests/modules/nf-core/picard/filtersamreads/**
-pirate:
-  - modules/nf-core/pirate/**
-  - tests/modules/nf-core/pirate/**
 plink/exclude:
   - modules/nf-core/plink/exclude/**
   - tests/modules/nf-core/plink/exclude/**

diff --git a/tests/modules/nf-core/pirate/main.nf b/tests/modules/nf-core/pirate/main.nf
diff --git a/tests/modules/nf-core/pirate/nextflow.config b/tests/modules/nf-core/pirate/nextflow.config
diff --git a/tests/modules/nf-core/pirate/test.yml b/tests/modules/nf-core/pirate/test.yml