From 3f0523ef88045b23862a28a261a11b07c1fe951a Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 18 Jul 2022 10:02:33 -0500
Subject: [PATCH] Add test workflows

---
 tests/modules/emboss/seqret/main.nf | 43 ++++++++++++++++++++++++++---
 1 file changed, 39 insertions(+), 4 deletions(-)

diff --git a/tests/modules/emboss/seqret/main.nf b/tests/modules/emboss/seqret/main.nf
index 2275c6c0..d3c703a2 100644
--- a/tests/modules/emboss/seqret/main.nf
+++ b/tests/modules/emboss/seqret/main.nf
@@ -3,13 +3,48 @@
 nextflow.enable.dsl = 2
 
 include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf'
+include { GUNZIP } from '../../../modules/gunzip/main.nf'
+
+workflow test_emboss_seqret_gb2embl {
 
-workflow test_emboss_seqret {
-    
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
     ]
 
-    EMBOSS_SEQRET ( input )
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'embl' )
+}
+
+workflow test_emboss_seqret_gb2gff {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'gff' )
+}
+
+workflow test_emboss_seqret_gb2pir {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'pir' )
+}
+
+workflow test_emboss_seqret_gb2fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true)
+    ]
+
+    GUNZIP ( input )
+    EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'fasta' )
 }