From 7275d6e87f4089660811743cffb3f2869231cb40 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 20 Oct 2023 10:49:41 +0200
Subject: [PATCH 1/2] add argument extreme_sensistity to fusioninspector

---
 CHANGELOG.md                          | 1 +
 conf/modules.config                   | 2 +-
 modules/local/fusioninspector/main.nf | 3 ++-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d67a99d5..91aea784 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)
 - Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420)
 - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420)
+- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering
 
 ### Fixed
 
diff --git a/conf/modules.config b/conf/modules.config
index 9a218711..a3366d44 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -102,7 +102,7 @@ process {
     withName: FUSIONINSPECTOR {
         ext.when = { !params.skip_vis }
         ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' }
-
+        ext.args2 = '--extreme_sensitivity'
     }
 
     withName: FUSIONREPORT {
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index 6f59a590..4d24a635 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -21,6 +21,7 @@ process FUSIONINSPECTOR {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def fasta = meta.single_end ? "--left_fq ${reads[0]}" : "--left_fq ${reads[0]} --right_fq ${reads[1]}"
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     """
     FusionInspector \\
         --fusions $fusion_list \\
@@ -29,7 +30,7 @@ process FUSIONINSPECTOR {
         --CPU ${task.cpus} \\
         -O . \\
         --out_prefix $prefix \\
-        --vis $args
+        --vis $args $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 0c471d171ff5a1b745f9d3377c0d33424c35cd93 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Fri, 20 Oct 2023 10:51:16 +0200
Subject: [PATCH 2/2] update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 91aea784..a18e6f9a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389)
 - Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420)
 - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420)
-- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering
+- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424)
 
 ### Fixed