add nf-test to samtools/faidx - nf-core#3936 (nf-core#5177)

* add nf-test to samtools/faidx

* delete old test files

* Update tags.yml

* change nextflow config to get good test inputs

---------

Co-authored-by: LE BARS Victor <[email protected]>
Co-authored-by: Louis LE NEZET <[email protected]>

modules/nf-core/samtools/faidx/environment.yml

@@ -1,8 +1,10 @@
 name: samtools_faidx
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::samtools=1.19.2
   - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.19.2

modules/nf-core/samtools/faidx/meta.yml

@@ -39,6 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - fa:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa}"
   - fai:
       type: file
       description: FASTA index file

modules/nf-core/samtools/faidx/tests/main.nf.test

@@ -0,0 +1,123 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_FAIDX"
+    script "../main.nf"
+    process "SAMTOOLS_FAIDX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/faidx"
+
+    test("test_samtools_faidx") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_fasta") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_stub_fasta") {
+
+        config "./nextflow2.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_stub_fai") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+}