From 92a7a0b242b09b719bb3fa479b40c26e78ed9512 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 23 Oct 2023 14:08:24 -0400
Subject: [PATCH] test: new tests for picard/samtofastq

---
 tests/modules/CCBR/picard/samtofastq/main.nf  |  9 +----
 .../CCBR/picard/samtofastq/nextflow.config    |  3 --
 tests/modules/CCBR/picard/samtofastq/test.yml | 34 +++++++++++++++++++
 3 files changed, 35 insertions(+), 11 deletions(-)
 create mode 100644 tests/modules/CCBR/picard/samtofastq/test.yml

diff --git a/tests/modules/CCBR/picard/samtofastq/main.nf b/tests/modules/CCBR/picard/samtofastq/main.nf
index ea6d348..547fb66 100644
--- a/tests/modules/CCBR/picard/samtofastq/main.nf
+++ b/tests/modules/CCBR/picard/samtofastq/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { PICARD_SAMTOFASTQ } from '../../../../../modules/nf-core/picard/samtofastq/main.nf'
+include { PICARD_SAMTOFASTQ } from '../../../../../modules/CCBR/picard/samtofastq/main.nf'
 
 workflow test_picard_samtofastq_single {
     input = [ [ id:'test', single_end: true ], // meta map
@@ -17,10 +17,3 @@ workflow test_picard_samtofastq_paired {
             ]
     PICARD_SAMTOFASTQ ( input )
 }
-
-workflow test_picard_samtofastq_paired_keep_unpaired {
-    input = [ [ id:'test', single_end: false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
-            ]
-    PICARD_SAMTOFASTQ ( input )
-}
diff --git a/tests/modules/CCBR/picard/samtofastq/nextflow.config b/tests/modules/CCBR/picard/samtofastq/nextflow.config
index 66840e0..8341169 100644
--- a/tests/modules/CCBR/picard/samtofastq/nextflow.config
+++ b/tests/modules/CCBR/picard/samtofastq/nextflow.config
@@ -1,7 +1,4 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    withName: "test_picard_samtofastq_paired_keep_unpaired" {
-        ext.args = "--UNPAIRED_FASTQ test.unpaired.fastq"
-    }
 }
diff --git a/tests/modules/CCBR/picard/samtofastq/test.yml b/tests/modules/CCBR/picard/samtofastq/test.yml
new file mode 100644
index 0000000..30a59a8
--- /dev/null
+++ b/tests/modules/CCBR/picard/samtofastq/test.yml
@@ -0,0 +1,34 @@
+- name: picard samtofastq test_picard_samtofastq_single
+  command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_single -c ./tests/config/nextflow.config
+  tags:
+    - picard/samtofastq
+    - picard
+  files:
+    - path: output/picard/test.fastq.gz
+      contains:
+        - "@ERR5069949.2151832"
+    - path: output/picard/versions.yml
+
+- name: picard samtofastq test_picard_samtofastq_paired
+  command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_paired -c ./tests/config/nextflow.config
+  tags:
+    - picard/samtofastq
+    - picard
+  files:
+    - path: output/picard/test_1.fastq.gz
+      contains:
+        - "@ERR5069949.2151832/1"
+    - path: output/picard/test_2.fastq.gz
+      contains:
+        - "@ERR5069949.2151832/2"
+    - path: output/picard/test.unpaired.fastq.gz
+    - path: output/picard/versions.yml
+
+- name: picard samtofastq test_picard_samtofastq_single stub
+  command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_single -c ./tests/config/nextflow.config -stub
+  tags:
+    - picard/samtofastq
+    - picard
+  files:
+    - path: output/picard/test.fastq.gz
+    - path: output/picard/versions.yml