Swap hicpca to nf-test (#7281)

* Swap hicpca to nf-test * Fix test * Update snapshot
nf-core · Jan 9, 2025 · 99b8a61 · 99b8a61
1 parent 667f74c
commit 99b8a61
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Showing 7 changed files with 225 additions and 37 deletions.
diff --git a/modules/nf-core/hicexplorer/hicpca/main.nf b/modules/nf-core/hicexplorer/hicpca/main.nf
@@ -37,20 +37,40 @@ process HICEXPLORER_HICPCA {
         args.remove(idx+1)
         args.remove(idx)
     }
-    outfilenames = eigenvectors.tokenize()
-        .collect{"${prefix}_pca${it}.${format}"}.join(' ')
+    outfilenames = eigenvectors.tokenize().collect{"${prefix}_pca${it}.${format}"}.join(' ')
     args = args.join(' ')
     """
     hicPCA \\
         -m $matrix \\
         $args \\
         --format $format \\
         --whichEigenvectors $eigenvectors \\
-        --outputFileName $outfilenames
+        --outputFileName ${outfilenames}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         hicexplorer: \$(hicPCA --version 2>&1 | sed 's/hicPCA //')
     END_VERSIONS
     """
+    stub:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    args     = args.tokenize()
+    def idx  = args.findIndexOf{ it == '--format' | it == '-f' }
+    format   = 'bigwig'
+    if (idx>=0) {
+        format = args[idx+1]
+        args.remove(idx+1)
+        args.remove(idx)
+    }
+    """
+    touch ${prefix}_pca1.${format}
+    touch ${prefix}_pca2.${format}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hicexplorer: \$(hicPCA --version 2>&1 | sed 's/hicPCA //')
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/hicexplorer/hicpca/tests/main.nf.test b/modules/nf-core/hicexplorer/hicpca/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process HICEXPLORER_HICPCA"
+    script "../main.nf"
+    process "HICEXPLORER_HICPCA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hicexplorer"
+    tag "hicexplorer/hicpca"
+
+    test("mm9 chr1") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file('https://github.com/deeptools/HiCExplorer/raw/master/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("mm9 chr1 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file('https://github.com/deeptools/HiCExplorer/raw/master/hicexplorer/test/test_data/hicPCA/mm9_reduced_chr1.cool', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/hicexplorer/hicpca/tests/main.nf.test.snap b/modules/nf-core/hicexplorer/hicpca/tests/main.nf.test.snap
@@ -0,0 +1,144 @@
+{
+    "mm9 chr1": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_pca1.bigwig:md5,e228fde481bedea641bcd0204bb663a4",
+                            "test_pca2.bigwig:md5,109c0d3cc70ecaf3647f3293504a9683"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca1.bigwig:md5,e228fde481bedea641bcd0204bb663a4"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca2.bigwig:md5,109c0d3cc70ecaf3647f3293504a9683"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,54775e8cd6ce193be8705000c3279192"
+                ],
+                "pca1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca1.bigwig:md5,e228fde481bedea641bcd0204bb663a4"
+                    ]
+                ],
+                "pca2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca2.bigwig:md5,109c0d3cc70ecaf3647f3293504a9683"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_pca1.bigwig:md5,e228fde481bedea641bcd0204bb663a4",
+                            "test_pca2.bigwig:md5,109c0d3cc70ecaf3647f3293504a9683"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54775e8cd6ce193be8705000c3279192"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-09T11:04:14.308469361"
+    },
+    "mm9 chr1 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_pca1.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_pca2.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca1.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca2.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,54775e8cd6ce193be8705000c3279192"
+                ],
+                "pca1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca1.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "pca2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_pca2.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_pca1.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_pca2.bigwig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54775e8cd6ce193be8705000c3279192"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-09T11:04:26.856478191"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -212,9 +212,6 @@ gridss/gridssgenerateponbedpe:
 gsea/gsea:
   - modules/nf-core/gsea/gsea/**
   - tests/modules/nf-core/gsea/gsea/**
-hicexplorer/hicpca:
-  - modules/nf-core/hicexplorer/hicpca/**
-  - tests/modules/nf-core/hicexplorer/hicpca/**
 hlala/preparegraph:
   - modules/nf-core/hlala/preparegraph/**
   - tests/modules/nf-core/hlala/preparegraph/**

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