From 14ade8060fbdff2097b3917e563940cdec58ee38 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 11:12:22 +0100
Subject: [PATCH] added preliminary pangolin test

---
 tests/software/pangolin/main.nf  | 12 ++++++++++++
 tests/software/pangolin/test.yml |  7 +++++++
 2 files changed, 19 insertions(+)
 create mode 100644 tests/software/pangolin/main.nf
 create mode 100644 tests/software/pangolin/test.yml

diff --git a/tests/software/pangolin/main.nf b/tests/software/pangolin/main.nf
new file mode 100644
index 00000000..e987d069
--- /dev/null
+++ b/tests/software/pangolin/main.nf
@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PANGOLIN } from '../../../software/pangolin/main.nf' addParams(options: [:])
+
+workflow test_pangolin {
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/../GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true) ] ]
+
+    PANGOLIN( input )
+}
diff --git a/tests/software/pangolin/test.yml b/tests/software/pangolin/test.yml
new file mode 100644
index 00000000..2f44feb4
--- /dev/null
+++ b/tests/software/pangolin/test.yml
@@ -0,0 +1,7 @@
+- name: pangolin
+  command: nextflow run ./tests/software/pangolin -profile docker -entry test_pangolin -c ./tests/config/nextflow.config
+  tags:
+    - pangolin
+  files:
+    - path: ./output/pangolin/test.lineage_report.csv
+      md5sum: a7423586a536a58f14fb4553f92b225e