From 835bc23b4feadfae00c0770bacf468b4f92ea966 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Fri, 8 Nov 2024 13:25:47 -0500
Subject: [PATCH] Improve guidance on WGS a bit.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 WGS-processing/cwl/wgs-processing-wf.cwl | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index ad88e6a..3a96f44 100644
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -7,10 +7,10 @@ doc: |
   alignment, and variant calling, returning GVCFs and accompanying
   clinvar variant reports.</p>
 
-  <p>The main parameter is <i>fastqdir</i>, which takes a directory
-  containing paired FASTQ files (suffixed with _1 and _2) to be
-  processed.  The workflow scatters over the samples to process them
-  in parallel.</p>
+  <p>The primary input parameter is the <b>Directory of paired FASTQ
+  files</b>, which should contain paired FASTQ files (suffixed with _1
+  and _2) to be processed.  The workflow scatters over the samples to
+  process them in parallel.</p>
 
   <p>The remaining parameters are reference data used by various tools
   in the pipeline.</p>
@@ -84,7 +84,7 @@ outputs:
       type: array
       items:
         type: array
-        items: File 
+        items: File
     outputSource: bwamem-gatk-report/qc-html
     format: edam:format_2331 # HTML
     label: FASTQ quality reports produced by fastqc
-- 
2.30.2