Merge branch 'master' into bump/gatk4

nf-core · Feb 14, 2024 · 000b48d · 000b48d
2 parents 14a62a5 + 6a3c74c
commit 000b48d
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diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test
@@ -0,0 +1,84 @@
+nextflow_process {
+
+    name "Test Process GATK4_REBLOCKGVCF"
+    script "../main.nf"
+    process "GATK4_REBLOCKGVCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/reblockgvcf"
+
+    test("test_gatk4_reblockgvcf") {
+        when {
+            process {
+                """
+                input[0] = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), []]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name, file(process.out.vcf.get(0).get(2)).name).match("test_gatk4_reblockgvcf") }
+            )
+        }
+
+    }
+
+    test("test_gatk4_reblockgvcf_intervals") {
+        when {
+            process {
+                """
+                input[0] = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name, file(process.out.vcf.get(0).get(2)).name).match("test_gatk4_reblockgvcf_intervals") }
+            )
+        }
+
+    }
+
+    test("test_gatk4_reblockgvcf_stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), []]
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name, file(process.out.vcf.get(0).get(2)).name).match("test_gatk4_reblockgvcf_stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap b/modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/reblockgvcf/tests/tags.yml b/modules/nf-core/gatk4/reblockgvcf/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/reblockgvcf:
+  - "modules/nf-core/gatk4/reblockgvcf/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -840,9 +840,6 @@ gatk4/printreads:
 gatk4/printsvevidence:
   - modules/nf-core/gatk4/printsvevidence/**
   - tests/modules/nf-core/gatk4/printsvevidence/**
-gatk4/reblockgvcf:
-  - modules/nf-core/gatk4/reblockgvcf/**
-  - tests/modules/nf-core/gatk4/reblockgvcf/**
 gatk4/revertsam:
   - modules/nf-core/gatk4/revertsam/**
   - tests/modules/nf-core/gatk4/revertsam/**

diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/main.nf b/tests/modules/nf-core/gatk4/reblockgvcf/main.nf
diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config b/tests/modules/nf-core/gatk4/reblockgvcf/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/reblockgvcf/test.yml b/tests/modules/nf-core/gatk4/reblockgvcf/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		gatk4/reblockgvcf:
		- "modules/nf-core/gatk4/reblockgvcf/**"