Make using COSMIC optional

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Use of only ensembl GTF file, not chr.gtf file as GTF reference file [#488](https://github.com/nf-core/rnafusion/pull/488)
 - Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
 - Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
+- Option to avoid using COSMIC (for example in the case of clinical use) [547](https://github.com/nf-core/rnafusion/pull/547)
 
 ### Changed
 
@@ -28,6 +29,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Remove fusionGDB from documentation and fusion-report download stubs [#503](https://github.com/nf-core/rnafusion/pull/503)
 
+### Parameters
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+|               | `--no_cosmic` |
+
 ## v3.0.2 - [2024-04-10]
 
 ### Added

conf/modules.config

@@ -97,7 +97,8 @@ process {
 
     withName: 'FUSIONREPORT' {
         ext.when         = { !params.skip_vis }
-        ext.args         = "--export csv"
+        ext.args         = { {params.no_cosmic} ? "--no-cosmic" : "" }
+        ext.args2        = "--export csv"
         publishDir = [
             path: { "${params.outdir}/fusionreport/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -106,7 +107,8 @@ process {
     }
 
     withName: 'FUSIONREPORT_DOWNLOAD' {
-        ext.args        = { params.qiagen ? "--qiagen" : "" }
+        ext.args         = { {params.no_cosmic} ? "--no-cosmic" : "" }
+        ext.args2        = { params.qiagen ? "--qiagen" : "" }
         publishDir = [
             path: { "${params.genomes_base}/fusion_report_db" },
             mode: params.publish_dir_mode,

docs/usage.md

@@ -49,6 +49,8 @@ nextflow run nf-core/rnafusion \
   --outdir <OUTPUT/PATH>
 ```
 
+If you are not covered by the research COSMIC license and want to avoid using COSMIC, you can provide the additional option `--no_cosmic`.
+
 ### Downloading the cosmic database with SANGER or QUIAGEN
 
 #### For academic users
@@ -156,6 +158,8 @@ nextflow run nf-core/rnafusion \
   --outdir <OUTPUT/PATH>
 ```
 
+If you are not covered by the research COSMIC license and want to avoid using COSMIC, you can provide the additional option `--no_cosmic`.
+
 > **IMPORTANT: Either `--all` or `--<tool>`** is necessary to run detection tools
 
 `--genomes_base` should be the path to the directory containing the folder `references/` that was built with `--build_references`.

modules/local/fusionreport/detect/main.nf

@@ -2,8 +2,7 @@ process FUSIONREPORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::star=2.7.9a"
-    container "docker.io/clinicalgenomics/fusion-report:2.1.8"
+    container "docker.io/clinicalgenomics/fusion-report:3.1.0"
 
 
     input:

modules/local/fusionreport/download/main.nf

@@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD {
     label 'process_medium'
 
     conda "bioconda::star=2.7.9a"
-    container "docker.io/clinicalgenomics/fusion-report:2.1.8"
+    container "docker.io/clinicalgenomics/fusion-report:3.1.0"
 
     input:
     val(username)
@@ -15,6 +15,7 @@ process FUSIONREPORT_DOWNLOAD {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
     """
     fusion_report download --cosmic_usr "$username" --cosmic_passwd "$passwd" $args ./
 

nextflow.config

@@ -73,6 +73,7 @@ params {
     skip_vis                   = false
 
     // Path to references
+    no_cosmic                     = false
     ensembl_ref                   = "${params.genomes_base}/ensembl"
     arriba_ref                    = "${params.genomes_base}/arriba"
     arriba_ref_blacklist          = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz"

nextflow_schema.json

@@ -348,6 +348,11 @@
                     "pattern": "^\\S+\\.interval_list?$",
                     "description": "Path to ribosomal interval list.",
                     "fa_icon": "far fa-file-code"
+                },
+                "no_cosmic": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Avoid using Cosmic DB (for example in clinical case applications where a paid license applies."
                 }
             }
         },