From 10628e0d5581191d1938c39abe7bcaed44e2717f Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 20 Jan 2025 15:18:29 +0100
Subject: [PATCH 1/2] update container fusionreport

---
 modules/local/fusionreport/detect/main.nf         | 5 ++++-
 modules/local/fusionreport/download/main.nf       | 6 ++++--
 subworkflows/local/fusioncatcher_workflow/main.nf | 4 ++--
 workflows/rnafusion.nf                            | 2 +-
 4 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf
index 56a29ab4..3670eec0 100644
--- a/modules/local/fusionreport/detect/main.nf
+++ b/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:
diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf
index 89f631db..ec62c75e 100644
--- a/modules/local/fusionreport/download/main.nf
+++ b/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
diff --git a/subworkflows/local/fusioncatcher_workflow/main.nf b/subworkflows/local/fusioncatcher_workflow/main.nf
index fd9ce34b..59614b61 100644
--- a/subworkflows/local/fusioncatcher_workflow/main.nf
+++ b/subworkflows/local/fusioncatcher_workflow/main.nf
@@ -9,7 +9,7 @@ workflow FUSIONCATCHER_WORKFLOW {
     take:
         reads                   // channel [ meta, [ fastqs ] ]
         fusioncatcher_ref       // channel [ meta, path       ]
-        run_fusioncatcher       // boolean
+        fusioncatcher       // boolean
         all                     // boolean
         fusioninspector_only    // boolean
         fusioncatcher_fusions   // path, string
@@ -18,7 +18,7 @@ workflow FUSIONCATCHER_WORKFLOW {
         ch_versions   = Channel.empty()
         ch_dummy_file = file("$baseDir/assets/dummy_file_fusioncatcher.txt", checkIfExists: true)
 
-        if (( run_fusioncatcher || all) && !fusioninspector_only ) {
+        if (( fusioncatcher || all) && !fusioninspector_only ) {
             if (fusioncatcher_fusions){
 
                 ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true)))
diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf
index ddd006ba..1cfa6cba 100644
--- a/workflows/rnafusion.nf
+++ b/workflows/rnafusion.nf
@@ -122,7 +122,7 @@ workflow RNAFUSION {
     FUSIONCATCHER_WORKFLOW (
         ch_reads,
         BUILD_REFERENCES.out.ch_fusioncatcher_ref,       // channel [ meta, path       ]
-        params.run_fusioncatcher,
+        params.fusioncatcher,
         params.all,
         params.fusioninspector_only,
         params.fusioncatcher_fusions

From 2c59f51c67b1a3da75d261600fb81808cda49e26 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 22 Jan 2025 11:39:19 +0100
Subject: [PATCH 2/2] fix path to process

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 967e820a..1a288a26 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -360,7 +360,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
+    withName: 'NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
         cpus   = { 24    * task.attempt }
         memory = { 100.GB * task.attempt }
         time   = { 2.d  * task.attempt }