From 51871ea6fca317ed6fca37597cabea895d62cbba Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 11:32:01 +0200
Subject: [PATCH 1/3] rnafusion setup for hasta usage

---
 conf/pipeline/rnafusion/hasta.config | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 conf/pipeline/rnafusion/hasta.config

diff --git a/conf/pipeline/rnafusion/hasta.config b/conf/pipeline/rnafusion/hasta.config
new file mode 100644
index 0000000..fdd7475
--- /dev/null
+++ b/conf/pipeline/rnafusion/hasta.config
@@ -0,0 +1,7 @@
+// rnafusion/hasta specific profile config for Clinical Genomics Stockholm usage
+
+params {
+    all = true
+    trim = true
+    fusioninspector_filter = true
+}

From 0851903f66068d4e05b43f6a296134098063a5a1 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:19:07 +0200
Subject: [PATCH 2/3] include new config in pipeline configs file

---
 README.md                        |  1 +
 docs/pipeline/rnafusion/hasta.md | 19 +++++++++++++++++++
 pipeline/rnafusion.config        |  4 +++-
 3 files changed, 23 insertions(+), 1 deletion(-)
 create mode 100644 docs/pipeline/rnafusion/hasta.md

diff --git a/README.md b/README.md
index 94ce55c..ae45869 100644
--- a/README.md
+++ b/README.md
@@ -198,6 +198,7 @@ Currently documentation is available for the following pipelines within specific
 - mag
   - [EVA](docs/pipeline/mag/eva.md)
 - rnafusion
+  - [HASTA](docs/pipeline/rnafusion/hasta.md)
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)
diff --git a/docs/pipeline/rnafusion/hasta.md b/docs/pipeline/rnafusion/hasta.md
new file mode 100644
index 0000000..9f7813d
--- /dev/null
+++ b/docs/pipeline/rnafusion/hasta.md
@@ -0,0 +1,19 @@
+# nf-core/configs: HASTA rnafusion specific configuration
+
+Extra specific configuration for rnafusion pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile hasta`.
+
+This will download and launch the rnafusion specific [`hasta.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `HASTA` cluster.
+
+Example: `nextflow run nf-core/rnafusion -profile hasta`
+
+## rnafusion specific configurations for HASTA
+
+Specific configurations for `HASTA` has been made for rnafusion.
+
+- Always run all the analysis steps (all = true)
+- Use trimming (trim = true)
+- Take the fusions identified by at least 2 fusion detection tools to the fusioninspector analysis (fusioninspector_filter = true)
diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config
index 2d86d89..f5a4e47 100644
--- a/pipeline/rnafusion.config
+++ b/pipeline/rnafusion.config
@@ -9,5 +9,7 @@
  */
 
 profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-}
\ No newline at end of file
+
+}

From 242101db16a342a45ef806e00ab20243327c4322 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 31 Aug 2022 14:26:32 +0200
Subject: [PATCH 3/3] fix extra space

---
 pipeline/rnafusion.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pipeline/rnafusion.config b/pipeline/rnafusion.config
index f5a4e47..894f6ab 100644
--- a/pipeline/rnafusion.config
+++ b/pipeline/rnafusion.config
@@ -11,5 +11,4 @@
 profiles {
   hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-
 }