Add first nf-test tests

guigolab · Apr 18, 2024 · 923014a · 923014a
1 parent 8aceb37
commit 923014a
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diff --git a/nf-test.config b/nf-test.config
@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "docker"
+
+}
diff --git a/tests/grape-pipeline-markdup.nf.test b/tests/grape-pipeline-markdup.nf.test
@@ -0,0 +1,29 @@
+nextflow_pipeline {
+
+    name "Test Workflow grape-pipeline.nf"
+    script "grape-pipeline.nf"
+
+    profile "+markdup"
+
+    test("Should run markdup pipeline") {
+
+
+        when {
+            params {
+                // define parameters here. Example: 
+                // outdir = "tests/results"
+                steps = 'mapping'
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.failed().size() == 0
+            assert workflow.trace.succeeded().size() == 20
+            def lines = file("${launchDir}/pipeline.db").readLines()
+            assert lines.size() == 9
+        }
+
+    }
+
+}
diff --git a/tests/grape-pipeline-starrsem.nf.test b/tests/grape-pipeline-starrsem.nf.test
@@ -0,0 +1,29 @@
+nextflow_pipeline {
+
+    name "Test Workflow grape-pipeline.nf"
+    script "grape-pipeline.nf"
+
+    profile "+starrsem"
+
+    test("Should run starrsem pipeline") {
+
+
+        when {
+            params {
+                // define parameters here. Example: 
+                // outdir = "tests/results"
+                steps = 'mapping'
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.failed().size() == 0
+            assert workflow.trace.succeeded().size() == 17
+            def lines = file("${launchDir}/pipeline.db").readLines()
+            assert lines.size() == 9
+        }
+
+    }
+
+}
diff --git a/tests/modules/fastaIndex/samtools/main.nf.test b/tests/modules/fastaIndex/samtools/main.nf.test
@@ -0,0 +1,28 @@
+nextflow_process {
+
+    name "Test Process fastaIndex"
+    script "modules/fastaIndex/samtools/main.nf"
+    process "fastaIndex"
+
+    test("Should produce the fasta index") {
+
+        when {
+            process {
+                """
+                input[0] = "${baseDir}/data/genome.fa"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+            with(process.out[0]) {
+              assert size() == 1
+              assert path(get(0)).md5 == "12d36d122df8dfe8fcfc96d78f785328"
+            }
+        }
+
+    }
+
+}
diff --git a/tests/modules/fastaIndex/samtools/main.nf.test.snap b/tests/modules/fastaIndex/samtools/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "Should produce the fasta index": {
+        "content": [
+            {
+                "0": [
+                    "genome.fa.fai:md5,12d36d122df8dfe8fcfc96d78f785328"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-16T11:50:45.127291"
+    }
+}
diff --git a/tests/modules/mapping/star/main.index.nf.test b/tests/modules/mapping/star/main.index.nf.test
@@ -0,0 +1,88 @@
+nextflow_process {
+
+    name "Test Process index"
+    script "modules/mapping/star/main.nf"
+    process "index"
+
+    test("Should index compressed references") {
+
+        when {
+            params {
+                sjOverHang = 100
+            }
+            process {
+                """
+                input[0] = file("${baseDir}/data/genome.fa.gz")
+                input[1] = file("${baseDir}/data/annotation.gtf.gz")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            with(process.out) {
+                def genomeDir = get(0)[0]
+                assert path(genomeDir).list().size() == 15
+                assert snapshot(
+                    path("${genomeDir}/Genome"),
+                    path("${genomeDir}/SA"),
+                    path("${genomeDir}/SAindex"),
+                    path("${genomeDir}/chrLength.txt"),
+                    path("${genomeDir}/chrName.txt"),
+                    path("${genomeDir}/chrNameLength.txt"),
+                    path("${genomeDir}/chrStart.txt"),
+                    path("${genomeDir}/exonGeTrInfo.tab"),
+                    path("${genomeDir}/exonInfo.tab"),
+                    path("${genomeDir}/geneInfo.tab"),
+                    path("${genomeDir}/genomeParameters.txt"),
+                    path("${genomeDir}/sjdbInfo.txt"),
+                    path("${genomeDir}/sjdbList.fromGTF.out.tab"),
+                    path("${genomeDir}/sjdbList.out.tab"),
+                    path("${genomeDir}/transcriptInfo.tab")
+                ).match()
+            }
+        }
+
+    }
+
+    test("Should index uncompressed references") {
+
+        when {
+            params {
+                sjOverHang = 100
+            }
+            process {
+                """
+                input[0] = file("${baseDir}/data/genome.fa")
+                input[1] = file("${baseDir}/data/annotation.gtf")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            with(process.out) {
+                def genomeDir = get(0)[0]
+                assert path(genomeDir).list().size() == 15
+                assert snapshot(
+                    path("${genomeDir}/Genome"),
+                    path("${genomeDir}/SA"),
+                    path("${genomeDir}/SAindex"),
+                    path("${genomeDir}/chrLength.txt"),
+                    path("${genomeDir}/chrName.txt"),
+                    path("${genomeDir}/chrNameLength.txt"),
+                    path("${genomeDir}/chrStart.txt"),
+                    path("${genomeDir}/exonGeTrInfo.tab"),
+                    path("${genomeDir}/exonInfo.tab"),
+                    path("${genomeDir}/geneInfo.tab"),
+                    path("${genomeDir}/genomeParameters.txt"),
+                    path("${genomeDir}/sjdbInfo.txt"),
+                    path("${genomeDir}/sjdbList.fromGTF.out.tab"),
+                    path("${genomeDir}/sjdbList.out.tab"),
+                    path("${genomeDir}/transcriptInfo.tab")
+                ).match()
+            }
+        }
+
+    }
+}
diff --git a/tests/modules/mapping/star/main.index.nf.test.snap b/tests/modules/mapping/star/main.index.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "Should index compressed references": {
+        "content": [
+            "Genome:md5,7ede3c93094305c2b5c18e2f52110194",
+            "SA:md5,66c24435d4e28eeddb6a5014ac90c4ef",
+            "SAindex:md5,71a85071f83b3df03194ded791487bd8",
+            "chrLength.txt:md5,d5218aeba91780be1b6e6d122fc16089",
+            "chrName.txt:md5,c6ae136a5ea0ebef9922c1e905c78e01",
+            "chrNameLength.txt:md5,5c6cc18be0eab93c65b0cf7d65ccdf40",
+            "chrStart.txt:md5,4ae3effcfe1d1c9d34fcf77a79f5e930",
+            "exonGeTrInfo.tab:md5,06545472694f13d808a021c152e407ae",
+            "exonInfo.tab:md5,a5d45fa06470ea940fee46b8278d98b7",
+            "geneInfo.tab:md5,c60a6703eaa7c4b75f4245eac7a659ab",
+            "genomeParameters.txt:md5,d32462a2f9c818b4245f57f3198ba83c",
+            "sjdbInfo.txt:md5,3bde943689ac279664d66d15b20a81c8",
+            "sjdbList.fromGTF.out.tab:md5,3204292dd60c21bc905145ec15e8f680",
+            "sjdbList.out.tab:md5,89ad4cd2dd4c868f6c32b29a57c376bb",
+            "transcriptInfo.tab:md5,3e6f9806497187a01ecbaaab6cce4f25"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-17T17:20:31.357378"
+    },
+    "Should index uncompressed references": {
+        "content": [
+            "Genome:md5,7ede3c93094305c2b5c18e2f52110194",
+            "SA:md5,66c24435d4e28eeddb6a5014ac90c4ef",
+            "SAindex:md5,71a85071f83b3df03194ded791487bd8",
+            "chrLength.txt:md5,d5218aeba91780be1b6e6d122fc16089",
+            "chrName.txt:md5,c6ae136a5ea0ebef9922c1e905c78e01",
+            "chrNameLength.txt:md5,5c6cc18be0eab93c65b0cf7d65ccdf40",
+            "chrStart.txt:md5,4ae3effcfe1d1c9d34fcf77a79f5e930",
+            "exonGeTrInfo.tab:md5,06545472694f13d808a021c152e407ae",
+            "exonInfo.tab:md5,a5d45fa06470ea940fee46b8278d98b7",
+            "geneInfo.tab:md5,c60a6703eaa7c4b75f4245eac7a659ab",
+            "genomeParameters.txt:md5,d32462a2f9c818b4245f57f3198ba83c",
+            "sjdbInfo.txt:md5,3bde943689ac279664d66d15b20a81c8",
+            "sjdbList.fromGTF.out.tab:md5,3204292dd60c21bc905145ec15e8f680",
+            "sjdbList.out.tab:md5,89ad4cd2dd4c868f6c32b29a57c376bb",
+            "transcriptInfo.tab:md5,3e6f9806497187a01ecbaaab6cce4f25"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-17T17:20:43.134729"
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -0,0 +1,15 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+
+params {
+  comprExts = ['gz', 'bz2', 'zip']
+}
+
+profiles {
+  docker {
+    docker.enabled = true
+  }
+}
diff --git a/tests/workflows/mapping.nf.test b/tests/workflows/mapping.nf.test
@@ -0,0 +1,79 @@
+nextflow_workflow {
+
+    name "Test Workflow mapping"
+    script "workflows/mapping.nf"
+    workflow "mapping"
+
+    test("Should run STAR mapping sorting with sambamba") {
+
+        when {
+            params {
+                mappingTool  = "STAR"
+                quantificationTool = "RSEM"
+                sortBamTool = "sambamba"
+                sjOverHang = 100
+                maxMismatches = 4
+                maxMultimaps = 10    
+            }
+            workflow {
+                """
+                input[0] = file("${baseDir}/data/genome.fa.gz")
+                input[1] = file("${baseDir}/data/annotation.gtf.gz")
+                input[2] = Channel.from(
+                    [
+                        [ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.out.genomeAlignments,
+                workflow.out.genomeAlignmentsIndices,
+                workflow.out.transcriptomeAlignments,
+                workflow.out.junctions
+            ).match()
+        }
+
+    }
+
+    test("Should run STAR mapping sorting with samtools") {
+
+        when {
+            params {
+                mappingTool  = "STAR"
+                quantificationTool = "RSEM"
+                sortBamTool = "samtools"
+                sjOverHang = 100
+                maxMismatches = 4
+                maxMultimaps = 10    
+            }
+            workflow {
+                """
+                input[0] = file("${baseDir}/data/genome.fa")
+                input[1] = file("${baseDir}/data/annotation.gtf")
+                input[2] = Channel.from(
+                    [
+                        [ "sample1", "test1", file("${baseDir}/data/test1_*.fastq.gz"), "fastq", ["fqRd1", "fqRd2"], '']
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.out.genomeAlignments,
+                workflow.out.genomeAlignmentsIndices,
+                workflow.out.transcriptomeAlignments,
+                workflow.out.junctions
+            ).match()
+        }
+
+    }
+
+}