Add nf-test for fusionreport_workflow subworkflow

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local subworkflow: `FUSIONCATCHER_WORKFLOW` [#591](https://github.com/nf-core/rnafusion/pull/591)
 - 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)
+- Add nf-test to local subworkflow: `FUSIONREPORT_WORKFLOW`. [#607](https://github.com/nf-core/rnafusion/pull/607)
 
 ### Changed
 

modules/local/fusionreport/detect/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fusion-report=3.1.1
+  - conda-forge::openpyxl=3.1.5

modules/local/fusionreport/detect/main.nf

@@ -2,7 +2,10 @@ process FUSIONREPORT {
     tag "$meta.id"
     label 'process_medium'
 
-    container "docker.io/clinicalgenomics/fusion-report:3.1.0"
+    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/d9/d9d1075dc45da6b08ec99c6e8bcc83e0ab71a674e7efdc7a36e459539793fcf9/data' :
+        'community.wave.seqera.io/library/fusion-report_openpyxl:6748677442b83a9a'}"
 
 
     input:

modules/local/fusionreport/download/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fusion-report=3.1.1
+  - conda-forge::openpyxl=3.1.5

modules/local/fusionreport/download/main.nf

@@ -2,8 +2,10 @@ process FUSIONREPORT_DOWNLOAD {
     tag 'fusionreport'
     label 'process_medium'
 
-    conda "bioconda::star=2.7.9a"
-    container "docker.io/clinicalgenomics/fusion-report:3.1.0"
+    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/d9/d9d1075dc45da6b08ec99c6e8bcc83e0ab71a674e7efdc7a36e459539793fcf9/data' :
+        'community.wave.seqera.io/library/fusion-report_openpyxl:6748677442b83a9a'}"
 
     output:
     tuple val(meta), path("fusion_report_db"), emit: fusionreport_ref

subworkflows/local/fusionreport_workflow.nf → subworkflows/local/fusionreport_workflow/main.nf

@@ -1,4 +1,4 @@
-include { FUSIONREPORT      }     from '../../modules/local/fusionreport/detect/main'
+include { FUSIONREPORT      }     from '../../../modules/local/fusionreport/detect/main'
 
 
 workflow FUSIONREPORT_WORKFLOW {

subworkflows/local/fusionreport_workflow/tests/main.nf.test

@@ -0,0 +1,77 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FUSIONREPORT_WORKFLOW"
+    script "../main.nf"
+    workflow "FUSIONREPORT_WORKFLOW"
+
+    tag "subworkflow"
+    tag "fusionreport_workflow"
+    tag "fusionreport"
+
+    test("FUSIONREPORT_WORKFLOW - Full Test") {
+
+        setup {
+            run("FUSIONREPORT_DOWNLOAD") {
+                script "../../../../modules/local/fusionreport/download/main.nf"
+                process {
+                    """
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                // Input channels
+                input[0] = Channel.of(
+                    [ [ id:'test_sample' ],
+                    file("https://github.com/nf-core/test-datasets/raw/rnafusion/testdata/human/reads_1.fq.gz") ]
+                )
+
+                input[1] = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref
+
+                input[2] = Channel.of(
+                    [[ id:'test_sample' ],
+                        file("https://github.com/Clinical-Genomics/fusion-report/raw/master/tests/test_data/arriba.tsv") ]
+                )
+
+                input[3] =  Channel.of(
+                    [[ id:'test_sample' ],
+                        file("https://github.com/Clinical-Genomics/fusion-report/raw/master/tests/test_data/starfusion.tsv") ]
+                )
+
+                input[4] =  Channel.of(
+                    [[ id:'test_sample' ],
+                        file("https://github.com/Clinical-Genomics/fusion-report/raw/master/tests/test_data/fusioncatcher.txt") ]
+                )
+
+                """
+            }
+            params {
+                fusioninspector_only = false
+                tools_cutoff = 1
+                arriba          = true
+                starfusion      = true
+                fusioncatcher   = true
+                no_cosmic       = true
+                outdir               = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.fusion_list,
+                    workflow.out.fusion_list_filtered,
+                    workflow.out.report,
+                    workflow.out.csv,
+                    workflow.out.versions
+                ).match() }
+            )
+        }
+    }
+
+
+}

subworkflows/local/fusionreport_workflow/tests/main.nf.test.snap

@@ -0,0 +1,46 @@
+{
+    "FUSIONREPORT_WORKFLOW - Full Test": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_sample"
+                    },
+                    "test_sample.fusionreport.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test_sample"
+                    },
+                    "test_sample.fusionreport_filtered.tsv:md5,3593b7021f26cc5427fdc96f0d1c72f0"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test_sample"
+                    },
+                    "test_sample_fusionreport_index.html:md5,3513bcaa58446399c0957db69402d3bd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test_sample"
+                    },
+                    "test_sample.fusions.csv:md5,49f378c2112d7e0b3b17d9095c79e6bd"
+                ]
+            ],
+            [
+                "versions.yml:md5,90749dbf8e3e7b259c935eabb8c6ce1e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-07T13:31:41.215356596"
+    }
+}

tests/.nftignore

@@ -33,3 +33,5 @@ starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Log.out
 starfusion/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm
 references/star/genomeParameters.txt
 starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt
+references/fusion_report_db/mitelman.db
+references/fusion_report_db/fusiongdb2.db

tests/test_build.nf.test.snap

@@ -279,6 +279,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-30T13:35:33.573499693"
+        "timestamp": "2025-01-14T13:08:24.564679638"
     }
-}
+}