From 7a61c04ed95649ef9505f15121757d09ba43a35d Mon Sep 17 00:00:00 2001
From: Thomas Rich <thomas.rich@nanoporetech.com>
Date: Wed, 27 Jul 2022 14:35:40 +0000
Subject: [PATCH] Update nextflow_schema.json

---
 .gitlab-ci.yml                                     | 2 +-
 nextflow_schema.json                               | 3 +++
 test_data/{SIRV_isofroms.gtf => SIRV_isoforms.gtf} | 0
 3 files changed, 4 insertions(+), 1 deletion(-)
 rename test_data/{SIRV_isofroms.gtf => SIRV_isoforms.gtf} (100%)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9c0ceb4..70c55df 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -9,4 +9,4 @@ variables:
     # Only common file inputs and option values need to be given here
     # (not things such as -profile)
     NF_WORKFLOW_OPTS: "--fastq test_data/fastq \
-      --ref_genome test_data/SIRV_150601a.fasta --ref_annotation test_data/SIRV_isofroms.gtf"
+      --ref_genome test_data/SIRV_150601a.fasta --ref_annotation test_data/SIRV_isoforms.gtf"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index af8db4b..b8aa3db 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -21,6 +21,7 @@
                 "fastq": {
                     "type": "string",
                     "format": "path",
+                    "demo_data": "${projectDir}/test_data/fastq",
                     "description": "A fastq file or directory containing fastq input files or directories of input files.",
                     "help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file."
                 },
@@ -41,11 +42,13 @@
                 "ref_genome": {
                     "type": "string",
                     "format": "file-path",
+                    "demo_data": "${projectDir}/test_data/SIRV_150601a.fasta",
                     "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow"
                 },
                 "ref_annotation": {
                     "type": "string",
                     "format": "file-path",
+                    "demo_data": "${projectDir}/test_data/SIRV_isoforms.gtf",
                     "description": "A reference annotation of gff format"
                 }
             },
diff --git a/test_data/SIRV_isofroms.gtf b/test_data/SIRV_isoforms.gtf
similarity index 100%
rename from test_data/SIRV_isofroms.gtf
rename to test_data/SIRV_isoforms.gtf