move gatk4/svcluster to nf-test (nf-core#4919)

RSC-RP · Mar 20, 2024 · cceb02b · cceb02b
1 parent 6d4a97b
commit cceb02b
Show file tree

Hide file tree

Showing 10 changed files with 76 additions and 75 deletions.
diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
+  - bioconda::gatk4=4.5.0.0
diff --git a/modules/nf-core/gatk4/svcluster/main.nf b/modules/nf-core/gatk4/svcluster/main.nf
@@ -4,8 +4,8 @@ process GATK4_SVCLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(indices)

diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test b/modules/nf-core/gatk4/svcluster/tests/main.nf.test
@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process GATK4_SVCLUSTER"
+    script "../main.nf"
+    process "GATK4_SVCLUSTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "manta"
+    tag "manta/germline"
+    tag "gatk4"
+    tag "gatk4/svcluster"
+
+    test("test_gatk4_svcluster") {
+        setup {
+            run("MANTA_GERMLINE") {
+                script "../../../manta/germline/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], []])
+                    input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)])
+                    input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)])
+                    input[3] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.combine(MANTA_GERMLINE.out.diploid_sv_vcf_tbi, by: 0)
+                input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/svcluster/samples_ploidy.tsv", checkIfExists:true)
+                input[2] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true))
+                input[3] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true))
+                input[4] = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true))
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.clustered_vcf.get(0).get(1)).name,
+                    process.out.clustered_vcf_index.get(0).get(1),
+                ).match("test_gatk4_svcluster") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap b/modules/nf-core/gatk4/svcluster/tests/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/svcluster/tests/nextflow.config b/modules/nf-core/gatk4/svcluster/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: MANTA_GERMLINE {
+            enabled: false
+        ]
+    }
+}
diff --git a/modules/nf-core/gatk4/svcluster/tests/tags.yml b/modules/nf-core/gatk4/svcluster/tests/tags.yml
@@ -0,0 +1,3 @@
+gatk4/svcluster:
+  - "modules/nf-core/gatk4/svcluster/**"
+  - "modules/nf-core/manta/germline/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -858,9 +858,6 @@ gatk4/splitcram:
 gatk4/splitintervals:
   - modules/nf-core/gatk4/splitintervals/**
   - tests/modules/nf-core/gatk4/splitintervals/**
-gatk4/svcluster:
-  - modules/nf-core/gatk4/svcluster/**
-  - tests/modules/nf-core/gatk4/svcluster/**
 gatk4/variantfiltration:
   - modules/nf-core/gatk4/variantfiltration/**
   - tests/modules/nf-core/gatk4/variantfiltration/**

diff --git a/tests/modules/nf-core/gatk4/svcluster/main.nf b/tests/modules/nf-core/gatk4/svcluster/main.nf
diff --git a/tests/modules/nf-core/gatk4/svcluster/nextflow.config b/tests/modules/nf-core/gatk4/svcluster/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/svcluster/test.yml b/tests/modules/nf-core/gatk4/svcluster/test.yml