Add nf-test to chromap/chromap (#5678)

* Add nf-test to chromap/chromap * Add nf-test to chromap/chromap (tags added) * Update modules/nf-core/chromap/chromap/tests/main.nf.test * Update modules/nf-core/chromap/chromap/tests/tags.yml * Update pytest_modules.yml * Update main.nf.test * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test.snap --------- Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
nf-core · May 22, 2024 · e37348c · e37348c
1 parent 0040936
commit e37348c
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Showing 8 changed files with 284 additions and 131 deletions.
diff --git a/modules/nf-core/chromap/chromap/tests/main.nf.test b/modules/nf-core/chromap/chromap/tests/main.nf.test
@@ -0,0 +1,145 @@
+nextflow_process {
+
+    name "Test Process CHROMAP_CHROMAP"
+    script "../main.nf"
+    process "CHROMAP_CHROMAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "chromap"
+    tag "chromap/chromap"
+    tag "chromap/index"
+
+    test("test_chromap_chromap_single_end") {
+
+        setup {
+            run("CHROMAP_INDEX") {
+                script "../../index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [:], // meta map
+                        [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
+                ])
+                input[1] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[2] = CHROMAP_INDEX.out.index
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_chromap_chromap_paired_end") {
+
+        setup {
+            run("CHROMAP_INDEX") {
+                script "../../index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [:], // meta map
+                        [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[2] = CHROMAP_INDEX.out.index
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_chromap_chromap_paired_bam") {
+
+        setup {
+            run("CHROMAP_INDEX") {
+                script "../../index/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [:], // meta map
+                        [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                    ])
+                    """
+                }
+            }
+        }
+
+        when {
+            config "./nextflow.config"
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
+                input[2] = CHROMAP_INDEX.out.index
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(file(process.out.bam[0][1]).name).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/chromap/chromap/tests/main.nf.test.snap b/modules/nf-core/chromap/chromap/tests/main.nf.test.snap
@@ -0,0 +1,130 @@
+{
+    "test_chromap_chromap_paired_end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed.gz:md5,54c1feb6f714b72f73befae8435e242b"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    "versions.yml:md5,80647c2956e504334ad25ce31d33b539"
+                ],
+                "bam": [
+
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed.gz:md5,54c1feb6f714b72f73befae8435e242b"
+                    ]
+                ],
+                "pairs": [
+
+                ],
+                "tagAlign": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,80647c2956e504334ad25ce31d33b539"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T19:08:55.497043"
+    },
+    "test_chromap_chromap_paired_bam": {
+        "content": [
+            "test.bam"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T19:09:02.957218"
+    },
+    "test_chromap_chromap_single_end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+                    "versions.yml:md5,80647c2956e504334ad25ce31d33b539"
+                ],
+                "bam": [
+
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed.gz:md5,c45f5bb1c6eb56359760ce3827bfe3f4"
+                    ]
+                ],
+                "pairs": [
+
+                ],
+                "tagAlign": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,80647c2956e504334ad25ce31d33b539"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T19:08:47.822066"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,80647c2956e504334ad25ce31d33b539"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T19:09:02.94685"
+    }
+}
diff --git a/modules/nf-core/chromap/chromap/tests/nextflow.config b/modules/nf-core/chromap/chromap/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: CHROMAP_CHROMAP {
+        ext.args = '--SAM'
+    }
+
+}
diff --git a/modules/nf-core/chromap/chromap/tests/tags.yml b/modules/nf-core/chromap/chromap/tests/tags.yml
@@ -0,0 +1,2 @@
+chromap/chromap:
+  - modules/nf-core/chromap/chromap/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -268,9 +268,6 @@ cellrangeratac/mkref:
 checkm/qa:
   - modules/nf-core/checkm/qa/**
   - tests/modules/nf-core/checkm/qa/**
-chromap/chromap:
-  - modules/nf-core/chromap/chromap/**
-  - tests/modules/nf-core/chromap/chromap/**
 circexplorer2/annotate:
   - modules/nf-core/circexplorer2/annotate/**
   - tests/modules/nf-core/circexplorer2/annotate/**

diff --git a/tests/modules/nf-core/chromap/chromap/main.nf b/tests/modules/nf-core/chromap/chromap/main.nf
diff --git a/tests/modules/nf-core/chromap/chromap/nextflow.config b/tests/modules/nf-core/chromap/chromap/nextflow.config