From 19ce9bdb9725b591d8a022d48188bb8d8327f850 Mon Sep 17 00:00:00 2001
From: Louis <louislenezet@gmail.com>
Date: Tue, 5 Mar 2024 13:51:38 +0100
Subject: [PATCH] Update simple test

---
 conf/test.config            | 10 ++++++++--
 tests/csv/sample_impute.csv |  3 +++
 2 files changed, 11 insertions(+), 2 deletions(-)
 create mode 100644 tests/csv/sample_impute.csv

diff --git a/conf/test.config b/conf/test.config
index fbb2e5c5..b03c69be 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -22,8 +22,14 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = "../test-datasets/data/bam.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome = "GRCh38"
+    panel  = "https://raw.githubusercontent.com/nf-core/test-datasets/imputation/data/panel/21/1000GP.chr21.noNA12878.s.bcf"
+    to_phase = false
+
+    // Impute parameters
+    step   = "impute"
+    tools  = "glimpse1"
 }
diff --git a/tests/csv/sample_impute.csv b/tests/csv/sample_impute.csv
new file mode 100644
index 00000000..bcf207f5
--- /dev/null
+++ b/tests/csv/sample_impute.csv
@@ -0,0 +1,3 @@
+sample,bam,bai
+NA12878,https://raw.githubusercontent.com/nf-core/test-datasets/imputation/data/NA12878/21/NA12878.chr21.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/imputation/data/NA12878/21/NA12878.chr21.s.1x.bam.bai
+NA12878_2,https://raw.githubusercontent.com/nf-core/test-datasets/imputation/data/NA12878/21/NA12878.chr21.s.1x.bam,https://raw.githubusercontent.com/nf-core/test-datasets/imputation/data/NA12878/21/NA12878.chr21.s.1x.bam.bai
\ No newline at end of file