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/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 +} 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..894f6ab 100644 --- a/pipeline/rnafusion.config +++ b/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" } -} \ No newline at end of file +}