nf-core · atrigila · Dec 26, 2024 · Dec 26, 2024 · Dec 26, 2024 · Dec 26, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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)
 - Add parameter `--references_only` when no data should be analysed, but only the references should be built [#505](https://github.com/nf-core/rnafusion/pull/505)
 - Add nf-test to local subworkflow: `STARFUSION_WORKFLOW`. [#597](https://github.com/nf-core/rnafusion/pull/597)
+- Add nf-test to local module: `FUSIONINSPECTOR`. [#601](https://github.com/nf-core/rnafusion/pull/601)
 
 ### Changed
 
@@ -40,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Integrate reference building in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
 - Move from ensembl to gencode base [#505](https://github.com/nf-core/rnafusion/pull/505)
 - Update from ensembl 102 to gencode 46 default references [#505](https://github.com/nf-core/rnafusion/pull/505)
+- Update`FUSIONINSPECTOR` to v2.10.0. [#601](https://github.com/nf-core/rnafusion/pull/601)
 - Remove local module `STARFUSION_DOWNLOAD` [#598](https://github.com/nf-core/rnafusion/pull/598)
 
 ### Fixed

diff --git a/conf/modules.config b/conf/modules.config
@@ -114,7 +114,7 @@ process {
         ]
     }
 
-    withName: 'FUSIONINSPECTOR' {
+    withName: '.*FUSIONINSPECTOR_WORKFLOW:.*:FUSIONINSPECTOR' {
         ext.when = { !params.skip_vis }
         ext.args = { ${params.fusioninspector_limitSjdbInsertNsj} != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }
         ext.args2 = '--annotate --examine_coding_effect'

diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
@@ -2,7 +2,11 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dfam=3.7
-  - bioconda::hmmer=3.4
-  - bioconda::minimap2=2.28
-  - bioconda::star-fusion=1.14.0
+  - bioconda::fusion-inspector=2.10.0
+  - bioconda::igv-reports=1.14.1
+  - bioconda::perl-json-xs=4.03
+  - bioconda::pysam=0.22.1
+  - conda-forge::perl-carp-assert=0.21
+  - pip
+  - pip:
+      - intervaltree==3.1.0
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
@@ -4,8 +4,8 @@ process FUSIONINSPECTOR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/13/139b94a1f10c6e23a8c27eaed1e5a689db978a513d0ee155e74d35f0970814fe/data' :
+        'community.wave.seqera.io/library/fusion-inspector_igv-reports_perl-json-xs_pysam_pruned:c6147971d107ab11'}"
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
@@ -15,7 +15,7 @@ process FUSIONINSPECTOR {
     tuple val(meta), path("*FusionInspector.fusions.tsv")                  , emit: tsv
     tuple val(meta), path("*.coding_effect")                , optional:true, emit: tsv_coding_effect
     tuple val(meta), path("*.gtf")                          , optional:true, emit: out_gtf
-    path "*"                                                               , emit: output
+    tuple val(meta), path("*FusionInspector.log")                          , emit: log
     path "versions.yml"                                                    , emit: versions
 
     when:

diff --git a/modules/local/fusioninspector/tests/main.nf.test b/modules/local/fusioninspector/tests/main.nf.test
@@ -0,0 +1,100 @@
+nextflow_process {
+
+    name "Test Process FUSIONINSPECTOR"
+    script "../main.nf"
+    process "FUSIONINSPECTOR"
+    tag "modules"
+    tag "modules_local"
+    tag "fusioninspector"
+
+    test("FUSIONINSPECTOR") {
+        config './nextflow.config'
+
+    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"
+                """
+            }
+        }
+    }
+
+        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
+                    [
+                        file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")
+                    ]
+                ]
+                input[1] = STARFUSION_BUILD.out.reference.map { it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.tsv[0][1]).name,
+                    process.out.tsv_coding_effect,  // TODO: These files do not seem to be produced. Consult Annick.
+                    process.out.out_gtf,            // TODO: These files do not seem to be produced. Consult Annick.
+                    file(process.out.log[0][1]).name,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("FUSIONINSPECTOR - stub") {
+
+        options "-stub"
+
+        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
+                    [
+                        file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")
+                    ]
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out).match() }
+            )
+        }
+
+    }
+
+
+}
diff --git a/modules/local/fusioninspector/tests/main.nf.test.snap b/modules/local/fusioninspector/tests/main.nf.test.snap
@@ -0,0 +1,111 @@
+{
+    "FUSIONINSPECTOR - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.fusions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.fusions.tsv.annotated.coding_effect:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "out_gtf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.fusions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tsv_coding_effect": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.FusionInspector.fusions.tsv.annotated.coding_effect:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-26T23:13:02.858688488"
+    },
+    "FUSIONINSPECTOR": {
+        "content": [
+            "test.FusionInspector.fusions.tsv",
+            [
+
+            ],
+            [
+
+            ],
+            "FusionInspector.log",
+            [
+                "versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-27T16:38:17.787825557"
+    }
+}
diff --git a/modules/local/fusioninspector/tests/nextflow.config b/modules/local/fusioninspector/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'FUSIONINSPECTOR' {
+        ext.args = '--annotate --examine_coding_effect'
+    }
+}