Merge pull request #669 from nf-core/container_fusioninspector

rannick · web-flow · commit e0c951b9d94e · 2025-06-02T09:36:22.000+02:00
Fixes for STARFUSION and FusionInspector
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -80,6 +80,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `fusioninspector`
   - `all` => This will automatically run all of the above tools
 - Updated all `wget` containers to `conda-forge::wget=1.21.4` [#655](https://github.com/nf-core/rnafusion/pull/655)
+- Using FusionInspector abridged output (that now contains coding effects) for downstream analysis [#669](https://github.com/nf-core/rnafusion/pull/669)
 
 ### Fixed
 
@@ -95,6 +96,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated the input validation to be more strict. This will prevent more errors down the line in the pipeline [#640](https://github.com/nf-core/rnafusion/pull/640)
 - The `FUSIONINSPECTOR` process will no longer fail when no fusions have been found. [#651](https://github.com/nf-core/rnafusion/pull/651)
 - Fixed STAR-Fusion build would fail when downloading Pfam and Dfam resources behind SSL. [#653](https://github.com/nf-core/rnafusion/pull/653)
+- Fix bug in argument handling for FusionInspector [#669](https://github.com/nf-core/rnafusion/pull/669)
 
 ### Removed
 
diff --git a/conf/modules.config b/conf/modules.config
@@ -103,7 +103,7 @@ process {
         ]
     }
 
-    withName: '.*FUSIONINSPECTOR_WORKFLOW:.*:FUSIONINSPECTOR' {
+    withName: 'FUSIONINSPECTOR' {
         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/main.nf b/modules/local/fusioninspector/main.nf
@@ -13,7 +13,6 @@ process FUSIONINSPECTOR {
 
     output:
     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
     tuple val(meta), path("*FusionInspector.log")                          , emit: log
     tuple val(meta), path("*html")                                         , emit: html
diff --git a/modules/local/fusioninspector/tests/main.nf.test b/modules/local/fusioninspector/tests/main.nf.test
@@ -25,7 +25,9 @@ nextflow_process {
                     ]
 
                     input[2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")
-                    input[3] = "human"
+                    input[3] = "homo_sapiens"
+                    input [4] = "3.8"
+                    input [5] = "37.4"
                     """
                 }
             }
@@ -44,7 +46,7 @@ nextflow_process {
                         file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")
                     ]
                 ]
-                input[1] = STARFUSION_BUILD.out.reference.map { it[1] }
+                input[1] = STARFUSION_BUILD.out.reference
                 """
             }
         }
@@ -128,7 +130,7 @@ nextflow_process {
                         file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")
                     ]
                 ]
-                input[1] = []
+                input[1] = [[id:'minigenome_refs'],[]]
                 """
             }
         }
diff --git a/modules/local/fusioninspector/tests/main.nf.test.snap b/modules/local/fusioninspector/tests/main.nf.test.snap
@@ -15,9 +15,6 @@
                     
                 ],
                 "2": [
-                    
-                ],
-                "3": [
                     [
                         {
                             "id": "test",
@@ -26,7 +23,7 @@
                         "test.FusionInspector.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "4": [
+                "3": [
                     [
                         {
                             "id": "test",
@@ -35,7 +32,7 @@
                         "test.fusion_inspector_web.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "5": [
+                "4": [
                     [
                         {
                             "id": "test",
@@ -44,7 +41,7 @@
                         "test.FusionInspector.fusions.abridged.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "6": [
+                "5": [
                     [
                         {
                             "id": "test",
@@ -73,7 +70,7 @@
                         ]
                     ]
                 ],
-                "7": [
+                "6": [
                     [
                         {
                             "id": "test",
@@ -133,7 +130,7 @@
                         ]
                     ]
                 ],
-                "8": [
+                "7": [
                     [
                         {
                             "id": "test",
@@ -186,7 +183,7 @@
                         ]
                     ]
                 ],
-                "9": [
+                "8": [
                     "versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"
                 ],
                 "abridged_tsv": [
@@ -369,9 +366,6 @@
                         },
                         "test.FusionInspector.fusions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "tsv_coding_effect": [
-                    
                 ],
                 "versions": [
                     "versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"
@@ -380,9 +374,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2024-12-31T13:48:13.020571472"
+        "timestamp": "2025-05-19T14:11:46.597061"
     },
     "FUSIONINSPECTOR": {
         "content": [
diff --git a/modules/local/fusioninspector/tests/nextflow.config b/modules/local/fusioninspector/tests/nextflow.config
@@ -1,5 +1,4 @@
 process {
     withName: 'FUSIONINSPECTOR' {
-        ext.args = '--annotate --examine_coding_effect'
-    }
+        ext.args = '--annotate --examine_coding_effect'    }
 }
diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf
@@ -46,7 +46,7 @@ workflow FUSIONINSPECTOR_WORKFLOW {
             AGAT_CONVERTSPGFF2TSV(FUSIONINSPECTOR.out.out_gtf)
             ch_versions = ch_versions.mix(AGAT_CONVERTSPGFF2TSV.out.versions)
 
-            fusion_data = FUSIONINSPECTOR.out.tsv_coding_effect.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out).join(fusionreport_csv)
+            fusion_data = FUSIONINSPECTOR.out.abridged_tsv.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)

Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@ process {`
`103`	`103`	`]`
`104`	`104`	`}`
`105`	`105`
`106`		`- withName: '.FUSIONINSPECTOR_WORKFLOW:.:FUSIONINSPECTOR' {`
	`106`	`+ withName: 'FUSIONINSPECTOR' {`
`107`	`107`	`ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }`
`108`	`108`	`ext.args2 = '--annotate --examine_coding_effect'`
`109`	`109`	`}`
Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,9 @@ nextflow_process {`
`25`	`25`	`]`
`26`	`26`
`27`	`27`	`input[2] = file("https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz")`
`28`		`- input[3] = "human"`
	`28`	`+ input[3] = "homo_sapiens"`
	`29`	`+ input [4] = "3.8"`
	`30`	`+ input [5] = "37.4"`
`29`	`31`	`"""`
`30`	`32`	`}`
`31`	`33`	`}`
`@@ -44,7 +46,7 @@ nextflow_process {`
`44`	`46`	`file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")`
`45`	`47`	`]`
`46`	`48`	`]`
`47`		`- input[1] = STARFUSION_BUILD.out.reference.map { it[1] }`
	`49`	`+ input[1] = STARFUSION_BUILD.out.reference`
`48`	`50`	`"""`
`49`	`51`	`}`
`50`	`52`	`}`
`@@ -128,7 +130,7 @@ nextflow_process {`
`128`	`130`	`file("https://github.com/FusionInspector/FusionInspector/raw/master/test/fusion_targets.A.txt")`
`129`	`131`	`]`
`130`	`132`	`]`
`131`		`- input[1] = []`
	`133`	`+ input[1] = [[id:'minigenome_refs'],[]]`
`132`	`134`	`"""`
`133`	`135`	`}`
`134`	`136`	`}`
Original file line number	Diff line number	Diff line change
`@@ -15,9 +15,6 @@`
`15`	`15`
`16`	`16`	`],`
`17`	`17`	`"2": [`
`18`		`-`
`19`		`- ],`
`20`		`- "3": [`
`21`	`18`	`[`
`22`	`19`	`{`
`23`	`20`	`"id": "test",`
`@@ -26,7 +23,7 @@`
`26`	`23`	`"test.FusionInspector.log:md5,d41d8cd98f00b204e9800998ecf8427e"`
`27`	`24`	`]`
`28`	`25`	`],`
`29`		`- "4": [`
	`26`	`+ "3": [`
`30`	`27`	`[`
`31`	`28`	`{`
`32`	`29`	`"id": "test",`
`@@ -35,7 +32,7 @@`
`35`	`32`	`"test.fusion_inspector_web.html:md5,d41d8cd98f00b204e9800998ecf8427e"`
`36`	`33`	`]`
`37`	`34`	`],`
`38`		`- "5": [`
	`35`	`+ "4": [`
`39`	`36`	`[`
`40`	`37`	`{`
`41`	`38`	`"id": "test",`
`@@ -44,7 +41,7 @@`
`44`	`41`	`"test.FusionInspector.fusions.abridged.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"`
`45`	`42`	`]`
`46`	`43`	`],`
`47`		`- "6": [`
	`44`	`+ "5": [`
`48`	`45`	`[`
`49`	`46`	`{`
`50`	`47`	`"id": "test",`
`@@ -73,7 +70,7 @@`
`73`	`70`	`]`
`74`	`71`	`]`
`75`	`72`	`],`
`76`		`- "7": [`
	`73`	`+ "6": [`
`77`	`74`	`[`
`78`	`75`	`{`
`79`	`76`	`"id": "test",`
`@@ -133,7 +130,7 @@`
`133`	`130`	`]`
`134`	`131`	`]`
`135`	`132`	`],`
`136`		`- "8": [`
	`133`	`+ "7": [`
`137`	`134`	`[`
`138`	`135`	`{`
`139`	`136`	`"id": "test",`
`@@ -186,7 +183,7 @@`
`186`	`183`	`]`
`187`	`184`	`]`
`188`	`185`	`],`
`189`		`- "9": [`
	`186`	`+ "8": [`
`190`	`187`	`"versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"`
`191`	`188`	`],`
`192`	`189`	`"abridged_tsv": [`
`@@ -369,9 +366,6 @@`
`369`	`366`	`},`
`370`	`367`	`"test.FusionInspector.fusions.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"`
`371`	`368`	`]`
`372`		`- ],`
`373`		`- "tsv_coding_effect": [`
`374`		`-`
`375`	`369`	`],`
`376`	`370`	`"versions": [`
`377`	`371`	`"versions.yml:md5,ad8d0da5929dfa70794bccf8765ddb23"`
`@@ -380,9 +374,9 @@`
`380`	`374`	`],`
`381`	`375`	`"meta": {`
`382`	`376`	`"nf-test": "0.9.2",`
`383`		`- "nextflow": "24.10.3"`
	`377`	`+ "nextflow": "25.04.2"`
`384`	`378`	`},`
`385`		`- "timestamp": "2024-12-31T13:48:13.020571472"`
	`379`	`+ "timestamp": "2025-05-19T14:11:46.597061"`
`386`	`380`	`},`
`387`	`381`	`"FUSIONINSPECTOR": {`
`388`	`382`	`"content": [`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,4 @@`
`1`	`1`	`process {`
`2`	`2`	`withName: 'FUSIONINSPECTOR' {`
`3`		`- ext.args = '--annotate --examine_coding_effect'`
`4`		`- }`
	`3`	`+ ext.args = '--annotate --examine_coding_effect' }`
`5`	`4`	`}`