From 45dc9efb4985a3815f886591ccc84d18dbec77af Mon Sep 17 00:00:00 2001
From: Sarah Griffiths <sarah.griffiths@nanoporetech.com>
Date: Fri, 8 Dec 2023 14:35:24 +0000
Subject: [PATCH] example cmd update

---
 nextflow.config | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 1bb98ab..900597e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -92,13 +92,16 @@ params {
 
     wf {
       example_cmd = [
-        "--condition_sheet 'wf-transcriptomes-demo/condition_sheet.tsv'",
+        "--de_analysis",
         "--direct_rna",
         "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
+        "--jaffal_annotation 'genCode22'",
+        "--jaffal_genome 'hg38_chr20'",
+        "--jaffal_refBase 'wf-transcriptomes-demo/chr20'",
         "--minimap2_index_opts '-k15'",
         "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
         "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
-        "--de_analysis",
+        "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"