Merge pull request #408 from nf-core/rnafusion_config_hasta

rnafusion setup for hasta usage [WIP]

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)

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
+}

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)

pipeline/rnafusion.config

@@ -9,5 +9,6 @@
  */
 
 profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/hasta.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnafusion/munin.config" }
-}
+}