Fix behavior when no fusion is present

CHANGELOG.md

@@ -118,6 +118,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix missing memory unit for fusioncatcher [#674](https://github.com/nf-core/rnafusion/pull/674)
 - Fix fusioncatcher download link [#693](https://github.com/nf-core/rnafusion/pull/693)
 - Fix fusionreport singularity container [#713](https://github.com/nf-core/rnafusion/pull/713)
+- Fix behavior when no fusion is present (log a warning and avoid running depending processes)[#714](https://github.com/nf-core/rnafusion/pull/714)
 - Fix CTAT-SPLICING output when no cancer introns were found [#722](https://github.com/nf-core/rnafusion/pull/722)
 - Update VCF_COLLECT script to adapt to transcript_version not being an entry in fusioninspector gtf anymore [#726](https://github.com/nf-core/rnafusion/pull/726)
 - Fix rRNA detection and make it more customizable with nf-core modules [#736](https://github.com/nf-core/rnafusion/pull/736)

modules/local/vcf_collect/main.nf

@@ -21,7 +21,6 @@ process VCF_COLLECT {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO use BGZIP to compress the VCF file instead of GZIP
     """
     vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --fusionreport_csv $fusionreport_csv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf
 

subworkflows/local/fusioninspector_workflow/main.nf

@@ -44,18 +44,30 @@ workflow FUSIONINSPECTOR_WORKFLOW {
         FUSIONINSPECTOR( ch_reads_fusion, ch_starfusion_ref)
         ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions)
 
-        if(!skip_vcf) {
-            AGAT_CONVERTSPGFF2TSV(FUSIONINSPECTOR.out.out_gtf)
+        def tsv_nonempty = FUSIONINSPECTOR.out.tsv.filter { _meta, file -> file.exists() && file.size() > 0 }
+        def tsv_abridged_nonempty = FUSIONINSPECTOR.out.abridged_tsv.filter { _meta, file -> file.exists() && file.size() > 0 }
+        def gtf_nonempty = FUSIONINSPECTOR.out.out_gtf.filter { _meta, file -> file.exists() && file.size() > 0 }
+        if (!tsv_nonempty) {
+            log.warn("FUSIONINSPECTOR confirmed no fusions, skipping VCF and visualisation steps.")
+        }
+        if (
+            !skip_vcf
+        ) {
+            AGAT_CONVERTSPGFF2TSV(gtf_nonempty)
             ch_versions = ch_versions.mix(AGAT_CONVERTSPGFF2TSV.out.versions)
 
-            fusion_data = FUSIONINSPECTOR.out.abridged_tsv.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out).join(fusionreport_csv)
+            fusion_data = tsv_abridged_nonempty
+                .join(AGAT_CONVERTSPGFF2TSV.out.tsv)
+                .join(fusionreport_out)
+                .join(fusionreport_csv)
 
             VCF_COLLECT(fusion_data, ch_hgnc_ref, ch_hgnc_date)
             ch_versions = ch_versions.mix(VCF_COLLECT.out.versions)
         }
-
-        if (!skip_vis) {
-            ch_bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv)
+        if (
+            !skip_vis
+        ){
+            ch_bam_sorted_indexed_fusions = bam_sorted_indexed.join(tsv_nonempty)
             ARRIBA_VISUALISATION(
                 ch_bam_sorted_indexed_fusions,
                 ch_gtf,

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

@@ -74,11 +74,11 @@ nextflow_workflow {
         when {
             params {
                 no_cosmic                  = true
-                whitelist                  = []
+                whitelist                  = ""
                 outdir                     = "test"
                 genomes_base               = "test"
                 fusionreport_download_args = '--no-cosmic'
-                fusionreport_detect_args   = {params.no_cosmic} ? "--no-cosmic" : ""
+                fusionreport_detect_args   = "--no-cosmic"
                 fusionreport_detect_args2  = "--export csv"
             }
             workflow {
@@ -94,31 +94,29 @@ nextflow_workflow {
                 input[2] = Channel.of([ [id:'test_sample'], file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")])
                 input[3] = FUSIONREPORT_DETECT.out.report
                 input[4] = FUSIONREPORT_DETECT.out.csv
-                input[5] = Channel.of([
-                    [id:'test_sample'],
-                    [],
-                    []
+                input[5] = Channel.of([[ id:'test', single_end:false ], // meta map
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam", checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai", checkIfExists: true)
                 ])
                 input[6] = Channel.of(
                     [ [ id:'test_gtf' ],
                     file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/minigenome.gtf')])
-                input[7] = Channel.of(file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3"))
-                input[8] = Channel.of(file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv"))
+                input[7] = Channel.fromPath("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3")
+                input[8] = Channel.fromPath("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv")
                 input[9] = Channel.of([[ id:'hgnc' ], file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/hgnc/hgnc_complete_set.txt")] )
                 input[10] = Channel.of([[ id:'hgnc_timestamp' ], file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/hgnc/HGNC-DB-timestamp.txt")] )
                 input[11] = STARFUSION_BUILD.out.reference
                 input[12] = false
                 input[13] = true
                 input[14] = 1
-                input[15] = []
+                input[15] = null
                 """
             }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(file(workflow.out.ch_arriba_visualisation[0][1]).length()) },
                 { assert snapshot(workflow.out.versions).match() }
             )
         }
@@ -183,11 +181,11 @@ nextflow_workflow {
         when {
             params {
                 no_cosmic                  = true
-                whitelist                  = []
+                whitelist                  = ""
                 outdir                     = "test"
                 genomes_base               = "test"
                 fusionreport_download_args = '--no-cosmic'
-                fusionreport_detect_args   = {params.no_cosmic} ? "--no-cosmic" : ""
+                fusionreport_detect_args   = "--no-cosmic"
                 fusionreport_detect_args2  = "--export csv"
             }
             workflow {
@@ -203,23 +201,22 @@ nextflow_workflow {
                 input[2] = Channel.of([ [id:'test_sample'], file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")])
                 input[3] = FUSIONREPORT_DETECT.out.report
                 input[4] = FUSIONREPORT_DETECT.out.csv
-                input[5] = Channel.of([
-                    [id:'test_sample'],
-                    [],
-                    []
+                input[5] = Channel.of([[ id:'test', single_end:false ], // meta map
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam", checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai", checkIfExists: true)
                 ])
                 input[6] = Channel.of(
                     [ [ id:'test_gtf' ],
                     file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/minigenome.gtf')])
-                input[7] = Channel.of(file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3"))
-                input[8] = Channel.of(file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv"))
+                input[7] = Channel.fromPath("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/protein_domains_hg38_GRCh38_v2.5.0.gff3")
+                input[8] = Channel.fromPath("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/arriba/cytobands_hg38_GRCh38_v2.5.0.tsv")
                 input[9] = Channel.of([[ id:'hgnc' ], file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/hgnc/hgnc_complete_set.txt")] )
                 input[10] = Channel.of([[ id:'hgnc_timestamp' ], file("https://github.com/nf-core/test-datasets/raw/refs/heads/rnafusion/testdata/reference/hgnc/HGNC-DB-timestamp.txt")] )
                 input[11] = STARFUSION_BUILD.out.reference
                 input[12] = false
                 input[13] = true
                 input[14] = 1
-                input[15] = params.whitelist
+                input[15] = null
                 """
             }
         }

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

@@ -3,48 +3,35 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test_sample"
-                        },
-                        "test_sample_combined_fusions_arriba_visualisation.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+
                 ],
                 "1": [
-                    "versions.yml:md5,01dce7699931b293311f2e5436b88a3a",
                     "versions.yml:md5,3be8e23309ed0bacebcad3d2fb30642a"
                 ],
                 "ch_arriba_visualisation": [
-                    [
-                        {
-                            "id": "test_sample"
-                        },
-                        "test_sample_combined_fusions_arriba_visualisation.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+
                 ],
                 "versions": [
-                    "versions.yml:md5,01dce7699931b293311f2e5436b88a3a",
                     "versions.yml:md5,3be8e23309ed0bacebcad3d2fb30642a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-26T20:11:13.798144726"
+        "timestamp": "2025-09-08T17:38:59.895142"
     },
     "FUSIONINSPECTOR_WORKFLOW - human": {
         "content": [
             [
-                "versions.yml:md5,01dce7699931b293311f2e5436b88a3a",
                 "versions.yml:md5,3be8e23309ed0bacebcad3d2fb30642a"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-28T21:54:05.453749443"
+        "timestamp": "2025-09-08T17:14:05.797063"
     }
 }

subworkflows/local/fusioninspector_workflow/tests/nextflow.config

@@ -3,14 +3,6 @@ process {
         ext.args = []
     }
 
-    withName: 'FUSIONREPORT_DOWNLOAD' {
-        ext.args         =  params.fusionreport_download_args
-    }
-
-    withName: 'FUSIONREPORT_DETECT' {
-        ext.args         = params.fusionreport_detect_args
-        ext.args2        = params.fusionreport_detect_args2
-    }
 
     withName: 'FUSIONINSPECTOR' {
         ext.args = '--annotate --examine_coding_effect'

subworkflows/local/qc_workflow/test/main.nf.test

@@ -61,7 +61,7 @@ nextflow_workflow {
                     input[1] = Channel.of(
                         [
                             [id: 'chr22_dict'],
-                            file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)
+                            file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict", checkIfExist: true)
                         ]
                     )
                     """
@@ -71,11 +71,10 @@ nextflow_workflow {
         }
 
         when {
-            // Params to activate modules ext.when condition
             params {
                 skip_qc              = false
                 fusioninspector_only = false
-                tools                = "starfusion"
+                tools               = "all"
                 outdir               = "test"
 
             }

tests/test_build.nf.test.snap

@@ -286,6 +286,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-05T12:58:07.878931"
+        "timestamp": "2025-09-09T11:45:13.886497"
     }
 }

tests/test_stub.nf.test.snap

@@ -561,20 +561,14 @@
     },
     "stub test fusioninspector": {
         "content": [
-            34,
+            31,
             {
                 "AGAT_CONVERTGFF2BED": {
                     "agat": "v1.5.1"
                 },
-                "AGAT_CONVERTSPGFF2TSV": {
-                    "agat": "v1.4.1"
-                },
                 "ARRIBA_ARRIBA": {
                     "arriba": "2.5.0"
                 },
-                "ARRIBA_VISUALISATION": {
-                    "arriba": "2.5.0"
-                },
                 "BIOAWK": {
                     "bioawk": 1.0
                 },
@@ -648,23 +642,16 @@
                 "UCSC_GTFTOGENEPRED": {
                     "ucsc": 447
                 },
-                "VCF_COLLECT": {
-                    "python": "3.11.0",
-                    "vcf_collect": 0.1
-                },
                 "Workflow": {
                     "nf-core/rnafusion": "v4.0.0dev"
                 }
             },
             [
                 "agat",
                 "agat/Homo_sapiens.GRCh38.46.gtf.bed",
-                "agat/test.tsv",
                 "arriba",
                 "arriba/test.arriba.fusions.discarded.tsv",
                 "arriba/test.arriba.fusions.tsv",
-                "arriba_visualisation",
-                "arriba_visualisation/test_combined_fusions_arriba_visualisation.pdf",
                 "bioawk",
                 "bioawk/Homo_sapiens.GRCh38.46.gtf_rrna.gtf.gz",
                 "fastqc",
@@ -840,9 +827,7 @@
                 "star/test.toTranscriptome.out.bam",
                 "star/test.unmapped_1.fastq.gz",
                 "star/test.unmapped_2.fastq.gz",
-                "star/testXd.out.bam",
-                "vcf",
-                "vcf/test_fusion_data.vcf"
+                "star/testXd.out.bam"
             ]
         ],
         "meta": {
@@ -1708,20 +1693,14 @@
     },
     "stub test all": {
         "content": [
-            45,
+            42,
             {
                 "AGAT_CONVERTGFF2BED": {
                     "agat": "v1.5.1"
                 },
-                "AGAT_CONVERTSPGFF2TSV": {
-                    "agat": "v1.4.1"
-                },
                 "ARRIBA_ARRIBA": {
                     "arriba": "2.5.0"
                 },
-                "ARRIBA_VISUALISATION": {
-                    "arriba": "2.5.0"
-                },
                 "BIOAWK": {
                     "bioawk": 1.0
                 },
@@ -1828,23 +1807,16 @@
                 "UCSC_GTFTOGENEPRED": {
                     "ucsc": 447
                 },
-                "VCF_COLLECT": {
-                    "python": "3.11.0",
-                    "vcf_collect": 0.1
-                },
                 "Workflow": {
                     "nf-core/rnafusion": "v4.0.0dev"
                 }
             },
             [
                 "agat",
                 "agat/Homo_sapiens.GRCh38.46.gtf.bed",
-                "agat/test.tsv",
                 "arriba",
                 "arriba/test.arriba.fusions.discarded.tsv",
                 "arriba/test.arriba.fusions.tsv",
-                "arriba_visualisation",
-                "arriba_visualisation/test_combined_fusions_arriba_visualisation.pdf",
                 "bioawk",
                 "bioawk/Homo_sapiens.GRCh38.46.gtf_rrna.gtf.gz",
                 "ctatsplicing",
@@ -2082,9 +2054,7 @@
                 "stringtie/test.ballgown",
                 "stringtie/test.coverage.gtf",
                 "stringtie/test.gene.abundance.txt",
-                "stringtie/test.transcripts.gtf",
-                "vcf",
-                "vcf/test_fusion_data.vcf"
+                "stringtie/test.transcripts.gtf"
             ]
         ],
         "meta": {