From 525d80984a88f9579604c8535d2942b607904fff Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 1 Aug 2023 16:38:27 +0200 Subject: [PATCH] Update documentation --- docs/usage.md | 2 ++ nextflow_schema.json | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 5b7f7aa6..02ec085a 100644 --- a/docs/usage.md +++ b/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,`. +> 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. diff --git a/nextflow_schema.json b/nextflow_schema.json index 0a4039f9..f5216d76 100644 --- a/nextflow_schema.json +++ b/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": {