Add stub and test to lofreq/indelqual

modules/nf-core/lofreq/indelqual/main.nf

@@ -33,4 +33,16 @@ process LOFREQ_INDELQUAL {
         lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/lofreq/indelqual/meta.yml

@@ -1,6 +1,8 @@
 name: lofreq_indelqual
 description: Inserts indel qualities in a BAM file
 keywords:
+  - variant calling
+  - variants
   - bam
   - indel
   - qualities
@@ -40,5 +42,6 @@ output:
       pattern: "*.{bam}"
 authors:
   - "@kaurravneet4123"
+  - "@krannich479"
 maintainers:
   - "@kaurravneet4123"

modules/nf-core/lofreq/indelqual/tests/main.nf.test

@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process LOFREQ_INDELQUAL"
+    script "../main.nf"
+    process "LOFREQ_INDELQUAL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "lofreq"
+    tag "lofreq/indelqual"
+
+    test("sarscov2 - bam, fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                input[1] = [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam, fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                input[1] = [
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}