Merge pull request #586 from atrigila/starfusion_detect

Add nf-test to local module `STARFUSION_DETECT`
nf-core · Dec 20, 2024 · a815895 · a815895
2 parents 3f4406a + 945bf0f
commit a815895
Show file tree

Hide file tree

Showing 5 changed files with 206 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572)
 - Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577)
 - Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
+- Add nf-test to local module: `STARFUSION_BUILD`. [#585](https://github.com/nf-core/rnafusion/pull/585)
+- Add nf-test to local module: `STARFUSION_DETECT`. [#586](https://github.com/nf-core/rnafusion/pull/586)
 - Added a new module `CTATSPLICING_STARTOCANCERINTRONS` and a new parameter `--ctatsplicing`. This options creates reports on cancer splicing abberations and requires one or both of `--arriba` and `--starfusion` to be given. [#587](https://github.com/nf-core/rnafusion/pull/587)
 
 ### Changed

diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
@@ -19,13 +19,14 @@ process STARFUSION {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def fasta = meta.single_end ? "--left_fq ${reads[0]}" : "--left_fq ${reads[0]} --right_fq ${reads[1]}"
+    def fastq_arg = reads ? (meta.single_end ? "--left_fq ${reads[0]}" : "--left_fq ${reads[0]} --right_fq ${reads[1]}") : ""
+    def junction_arg =  junction ? "-J ${junction}" : ""
     def args = task.ext.args ?: ''
     """
     STAR-Fusion \\
         --genome_lib_dir $reference \\
-        $fasta \\
-        -J $junction \\
+        $fastq_arg \\
+        $junction_arg \\
         --CPU $task.cpus \\
         --examine_coding_effect \\
         --output_dir . \\

diff --git a/modules/local/starfusion/detect/tests/main.nf.test b/modules/local/starfusion/detect/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process STARFUSION"
+    script "../main.nf"
+    process "STARFUSION"
+
+    setup {
+        run("STARFUSION_BUILD") {
+            script "../../../starfusion/build/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'minigenome fasta' ],
+                    file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa")
+                ]
+                input[1] = [
+                    [ id:'minigenome gtf' ],
+                    file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf")
+                ]
+
+                input [2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")
+                input [3] = "human"
+                """
+            }
+        }
+    }
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_1.fastq.gz"),
+                        file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_2.fastq.gz")
+                    ], // reads
+                    [] // empty list for junction, as we don't have a pre-computed Chimeric.out.junction file
+                ]
+                input[1] = STARFUSION_BUILD.out.reference.map { it[1] }
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out.fusions,
+                process.out.abridged,
+                process.out.coding_effect,
+                process.out.versions
+            ).match()
+        }
+
+    }
+
+    test("Should create stub files") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_stub', single_end:false ],
+                    [
+                        file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_1.fastq.gz"),
+                        file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/v0.0.1/rnaseq_2.fastq.gz")
+                    ],
+                    [] // empty list for junction
+                ]
+                input[1] = STARFUSION_BUILD.out.reference.map { it[1] }
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                process.out
+            ).match()
+        }
+
+    }
+
+}
diff --git a/modules/local/starfusion/detect/tests/main.nf.test.snap b/modules/local/starfusion/detect/tests/main.nf.test.snap
@@ -0,0 +1,112 @@
+{
+    "Should create stub files": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.fusion_predictions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.abridged.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.abridged.coding_effect.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,a8fb6344fdf740dde0941048313fc243"
+                ],
+                "abridged": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.abridged.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "coding_effect": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.abridged.coding_effect.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fusions": [
+                    [
+                        {
+                            "id": "test_stub",
+                            "single_end": false
+                        },
+                        "test_stub.starfusion.fusion_predictions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a8fb6344fdf740dde0941048313fc243"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-19T18:42:06.988178092"
+    },
+    "Should run without failures": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.starfusion.fusion_predictions.tsv:md5,82834fffed743afe07da82bd56d50c99"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.starfusion.abridged.tsv:md5,d6d20fdd4b5cba21b9c0ebf8e0ea19ff"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.starfusion.abridged.coding_effect.tsv:md5,95dfce6fdaf3589f23881fe1e855c62b"
+                ]
+            ],
+            [
+                "versions.yml:md5,a8fb6344fdf740dde0941048313fc243"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-19T18:41:49.150362156"
+    }
+}
diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf
@@ -34,7 +34,7 @@ workflow STARFUSION_WORKFLOW {
                 SAMTOOLS_INDEX_FOR_STARFUSION(STAR_FOR_STARFUSION.out.bam_sorted)
                 ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_STARFUSION.out.versions)
                 bam_sorted_indexed = STAR_FOR_STARFUSION.out.bam_sorted.join(SAMTOOLS_INDEX_FOR_STARFUSION.out.bai)
-                reads_junction = reads.join(STAR_FOR_STARFUSION.out.junction )
+                reads_junction = reads.join(STAR_FOR_STARFUSION.out.junction )  // TODO: This join is not needed as STARFUSION can simply read from the junction file: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
 
                 if (params.ctatsplicing || params.all) {
                     CTATSPLICING_WORKFLOW(