testing if it works with just fastq

nf-core · Jan 19, 2025 · e32bbb0 · e32bbb0
1 parent 1f6b509
commit e32bbb0
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Showing 2 changed files with 17 additions and 23 deletions.
diff --git a/modules/nf-core/fast2q/tests/main.nf.test b/modules/nf-core/fast2q/tests/main.nf.test
@@ -10,23 +10,23 @@ nextflow_process {
 
     config './nextflow.config'
 
-    test("FASTQ file with optional library") {
-
+    test("Extracting all features at position=0 with default length of 20bp from a FASTQ file (without optional library.csv)") {
+        
         when {
-
+            
             params {
-                module_args = '-c'
+                module_args = '--mo EC'
             }
 
             process {
                 """
                 input[0] = [
                     [ id:'test1', single_end:true ], // meta map
-                    file(params.modules_testdata_base_path + '/example.fastq.gz', checkIfExists: true) // FASTQ file
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
                 ]
                 input[1] = [
                     [ id:'test2', single_end:true ], // meta map for second input
-                    file(params.modules_testdata_base_path + '/D39V_guides.csv', checkIfExists: true) // library file
+                    []
                 ]
                 """
             }
@@ -42,19 +42,19 @@ nextflow_process {
 
     }
 
-    test("Extracting all features at position=0 with default length of 20bp from a FASTQ file (without optional library.csv)") {
-        
+    test("2FAST2Q self-test") {
+
         when {
-            
+
             params {
-                module_args = '-c --mo EC'
-            }
+            module_args = '-t'
+                }
 
             process {
                 """
                 input[0] = [
                     [ id:'test1', single_end:true ], // meta map
-                    file(params.modules_testdata_base_path + '/example.fastq.gz', checkIfExists: true) // FASTQ file
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
                 ]
                 input[1] = [
                     [ id:'test2', single_end:true ], // meta map for second input
@@ -74,23 +74,19 @@ nextflow_process {
 
     }
 
-        test("2FAST2Q self-test") {
+    /* test("FASTQ file with optional library") {
 
         when {
 
-            params {
-            module_args = '-c -t'
-                }
-
             process {
                 """
                 input[0] = [
                     [ id:'test1', single_end:true ], // meta map
-                    file(params.modules_testdata_base_path + '/example.fastq.gz', checkIfExists: true) // FASTQ file
+                    file(params.modules_testdata_base_path + '/SRR8983579.small.fastq.gz', checkIfExists: true) // FASTQ file
                 ]
                 input[1] = [
                     [ id:'test2', single_end:true ], // meta map for second input
-                    []
+                    file(params.modules_testdata_base_path + '/D39V_guides.csv', checkIfExists: true) // library file
                 ]
                 """
             }
@@ -103,7 +99,6 @@ nextflow_process {
                 { assert path(process.out.versions).readLines().join("\n").contains("2FAST2Q version") } // Verify version output
             )
         }
-
-    }
+    } */
 
 }
diff --git a/modules/nf-core/fast2q/tests/nextflow.config b/modules/nf-core/fast2q/tests/nextflow.config
@@ -1,6 +1,5 @@
 params {
-    //modules_testdata_base_path = "https://github.com/nf-core/test-datasets/tree/crisprseq/testdata"
-    modules_testdata_base_path = "https://github.com/afombravo/2FAST2Q/blob/main/"
+    modules_testdata_base_path = "https://github.com/nf-core/test-datasets/tree/crisprseq/testdata"
     module_args = '' // Default to an empty string
 }