From 8c61d4f2432f830499f0879b523aff100fcc3ad2 Mon Sep 17 00:00:00 2001
From: Francesco L <francesco.lescai@unipv.it>
Date: Sun, 14 Jan 2024 09:46:55 +0100
Subject: [PATCH] added usage doc for cnvkit targets

---
 docs/usage.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/docs/usage.md b/docs/usage.md
index 1bc6a75..829ae4e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -114,6 +114,27 @@ If you are running the pipeline to generate references for the GATK's germlinecn
 
 <sup>1</sup> To learn more about this file, see [this comment](https://gatk.broadinstitute.org/hc/en-us/community/posts/360074399831/comments/13441240230299) on GATK forum.<br />
 
+
+### cnvkit
+
+If you are running the pipeline to generate references for the CNVkit variant calling workflow, you should consider that currently the default method for this pipeline is whole-genome. In order to use the CNVkit default, i.e. hybrid capture, when the user is creating a background for targeted capture sequencing (most commonly, exomes or panels), the user should
+
+1. provide an additional config file, in order to change or remove the method specified in the default `ext.args`, i.e.
+
+```
+process {
+
+    withName: CNVKIT_BATCH {
+        ext.args   = {"--output-reference ${meta.id}.cnn"}
+    }
+
+}
+```
+
+2. provide the `--cnvkit_target` parameter (optional) as a .bed file for the targets
+
+
+
 ## Core Nextflow arguments
 
 > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).