Merge pull request #394 from genomic-medicine-sweden/variantcatalogdocs

Update documentation

docs/usage.md

@@ -71,6 +71,8 @@ work                # Directory containing the Nextflow working files
 
 Test profile runs the pipeline with a case containing three samples, but if you would like to test the pipeline with one sample, use `-profile test_one_sample,<YOURPROFILE>`.
 
+> Note that the default cpu and memory configurations used in raredisease are written keeping the test profile (&dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform.
+
 ### Updating the pipeline
 
 The above command downloads the pipeline from GitHub, caches it, and tests it on the test dataset. When you run the command again, it will fetch the pipeline from cache even if a more recent version of the pipeline is available. To make sure that you're running the latest version of the pipeline, update the cached version of the pipeline by including `-latest` in the command.

nextflow_schema.json

@@ -310,7 +310,7 @@
                     "exists": true,
                     "format": "file-path",
                     "description": "Path to variant catalog file",
-                    "help_text": "Used with ExpansionHunter and if no catalogue is passed, then a default will be used.",
+                    "help_text": "Should be Stranger's extended JSON as described at https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json. This file is used by both ExpansionHunter and Stranger",
                     "fa_icon": "fas fa-file"
                 },
                 "vcfanno_resources": {