Bump phantompeakqualtools 1.2.2 (#5889)

* Add stub section * Update yml * Add nf-test * Get rid of pytest * Make lint happy * Update tests * Update tests to make lint happy * update tests * Make lint happy * Using the same version as CI of nf-test locally might be a good idea * Use wave images * Make lint happy * Simplify tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
nf-core · Jun 27, 2024 · 2dfe9af · 2dfe9af
1 parent 0aef8ea
commit 2dfe9af
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Showing 10 changed files with 232 additions and 61 deletions.
diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml
@@ -1,7 +1,9 @@
-name: phantompeakqualtools
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "phantompeakqualtools"
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - bioconda::phantompeakqualtools=1.2.2
+  - "bioconda::phantompeakqualtools=1.2.2"
diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf
@@ -5,8 +5,8 @@ process PHANTOMPEAKQUALTOOLS {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' :
-        'biocontainers/phantompeakqualtools:1.2.2--0' }"
+        'oras://community.wave.seqera.io/library/phantompeakqualtools:1.2.2--50be7727b2a72700' :
+        'community.wave.seqera.io/library/phantompeakqualtools:1.2.2--f8026fe2526a5e18' }"
 
     input:
     tuple val(meta), path(bam)
@@ -34,4 +34,18 @@ process PHANTOMPEAKQUALTOOLS {
         phantompeakqualtools: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.spp.pdf
+    touch ${prefix}.spp.Rdata
+    touch ${prefix}.spp.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        phantompeakqualtools: $VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml
@@ -18,7 +18,7 @@ tools:
       documentation: "https://github.com/kundajelab/phantompeakqualtools"
       tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools"
       doi: "10.1101/gr.136184.111"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test b/modules/nf-core/phantompeakqualtools/tests/main.nf.test
@@ -0,0 +1,90 @@
+// nf-core modules test phantompeakqualtools
+nextflow_process {
+
+    name "Test Process PHANTOMPEAKQUALTOOLS"
+    script "../main.nf"
+    process "PHANTOMPEAKQUALTOOLS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "phantompeakqualtools"
+
+    test("sarscov2 - bam - single_end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.spp,
+                                  file(process.out.pdf.get(0).get(1)).name,
+                                  file(process.out.rdata.get(0).get(1)).name,
+                                  process.out.versions)
+                                  .match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - paired_end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.spp,
+                                  file(process.out.pdf.get(0).get(1)).name,
+                                  file(process.out.rdata.get(0).get(1)).name,
+                                  process.out.versions)
+                                  .match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap
@@ -0,0 +1,119 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.Rdata:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc"
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "rdata": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.Rdata:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "spp": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.spp.out:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-27T10:46:22.786363"
+    },
+    "sarscov2 - bam - single_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.spp.out:md5,b01d976506b6fe45b66c821b1e8a1d15"
+                ]
+            ],
+            "test.spp.pdf",
+            "test.spp.Rdata",
+            [
+                "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-27T16:21:12.000709154"
+    },
+    "sarscov2 - bam - paired_end": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.spp.out:md5,eed46e75eab119224f397a7a8b5924e6"
+                ]
+            ],
+            "test.spp.pdf",
+            "test.spp.Rdata",
+            [
+                "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-27T16:21:22.432426907"
+    }
+}
diff --git a/modules/nf-core/phantompeakqualtools/tests/tags.yml b/modules/nf-core/phantompeakqualtools/tests/tags.yml
@@ -0,0 +1,2 @@
+phantompeakqualtools:
+  - "modules/nf-core/phantompeakqualtools/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1181,9 +1181,6 @@ pbptyper:
 peka:
   - modules/nf-core/peka/**
   - tests/modules/nf-core/peka/**
-phantompeakqualtools:
-  - modules/nf-core/phantompeakqualtools/**
-  - tests/modules/nf-core/phantompeakqualtools/**
 phyloflash:
   - modules/nf-core/phyloflash/**
   - tests/modules/nf-core/phyloflash/**

diff --git a/tests/modules/nf-core/phantompeakqualtools/main.nf b/tests/modules/nf-core/phantompeakqualtools/main.nf
diff --git a/tests/modules/nf-core/phantompeakqualtools/nextflow.config b/tests/modules/nf-core/phantompeakqualtools/nextflow.config
diff --git a/tests/modules/nf-core/phantompeakqualtools/test.yml b/tests/modules/nf-core/phantompeakqualtools/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		phantompeakqualtools:
		- "modules/nf-core/phantompeakqualtools/**"