4451 add vcf2maf nf test (nf-core#4463)

* add nf-test case for vcf2maf without VEP

* add VEP test case for vcf2maf nf-test

* update linting for vcf2maf

* fix prettier for vcf2maf

* remove pytest files for vcf2maf

* remove vcf2maf from pytest modules yml

* add modules/nf-core/vcf2maf/tests/tags.yml

* add line count to vcf2maf test

* add line number and versions contents yaml to vcf2maf test

* remove alternate container from vcf2maf testing and use the same container for testing with or without VEP

* update modules/nf-core/vcf2maf/tests/main.nf.test

* update modules/nf-core/vcf2maf/tests/main.nf.test

* Update and fix tests

* Apply suggestions from code review

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Add conda declaration to nf-test

* Remove output in snapshot

* Add versions to snapshot

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

modules/nf-core/vcf2maf/environment.yml

@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::vcf2maf=1.6.21
   - bioconda::ensembl-vep=106.1
+  - bioconda::vcf2maf=1.6.21

modules/nf-core/vcf2maf/tests/main.nf.test

@@ -0,0 +1,76 @@
+nextflow_process {
+    name "Test vcf2maf"
+    process "VCF2MAF"
+    script "../main.nf"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vcf2maf"
+    tag "untar"
+
+    test("Run without VEP") {
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test'], // meta map
+                                file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true)
+                            ]
+                input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ]
+                input[2] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.maf[0][1]).readLines()[5..131],
+                    process.out.versions
+                ).match() },
+                { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', '    vcf2maf: 1.6.21', '    ensemblvep: 106.1'] }
+            )
+        }
+    }
+
+    test("Run with VEP"){
+        tag "vcf2maf-withVEP"
+        config "./nextflow.withVEP.config"
+
+        setup {
+            run("UNTAR") {
+                script "../../../../modules/nf-core/untar/main.nf"
+                process {
+                """
+                input[0] = [ 
+                    [ id:'test_genome_vep' ], 
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vep.tar.gz", checkIfExists: true) 
+                ]
+                """
+            }
+        }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test'], // meta map
+                                file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true)
+                            ]
+                input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ]
+                input[2] = UNTAR.out.untar.map { it[1] }
+                """
+            }
+        }
+
+        then{
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines
+                { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', '    vcf2maf: 1.6.21', '    ensemblvep: 106.1'] }
+            )
+        }
+    }
+}

modules/nf-core/vcf2maf/tests/nextflow.config

@@ -0,0 +1,11 @@
+// config for running without VEP
+params.species = "homo_sapiens"
+params.build   = "GRCh38"
+
+process {
+    container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0"
+    conda = "bioconda::vcf2maf=1.6.21"
+    withName: 'VCF2MAF' {  
+        ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep"  
+    }
+}

modules/nf-core/vcf2maf/tests/nextflow.withVEP.config

@@ -0,0 +1,9 @@
+// config for running with VEP
+params.species = "homo_sapiens"
+params.build   = "GRCh38"
+
+process {
+    withName: 'VCF2MAF' {
+        ext.args = "--ncbi-build ${params.build} --species ${params.species}"
+    }
+}

modules/nf-core/vcf2maf/tests/tags.yml

@@ -0,0 +1,2 @@
+vcf2maf:
+  - modules/nf-core/vcf2maf/**

tests/config/nextflow.config

@@ -16,9 +16,11 @@ if ("$PROFILE" == "singularity") {
     singularity.autoMounts = true
 } else if ("$PROFILE" == "conda") {
     conda.enabled = true
+    conda.useMicromamba = true
 } else if ("$PROFILE" == "mamba") {
     conda.enabled  = true
     conda.useMamba = true
+    conda.useMicromamba = true
 } else if ("$PROFILE" == "podman") {
     podman.enabled = true
     podman.userEmulation = true

tests/config/pytest_modules.yml

@@ -813,9 +813,9 @@ varlociraptor/callvariants:
 varlociraptor/preprocess:
   - modules/nf-core/varlociraptor/preprocess/**
   - tests/modules/nf-core/varlociraptor/preprocess/**
-vcf2maf:
-  - modules/nf-core/vcf2maf/**
-  - tests/modules/nf-core/vcf2maf/**
+vcflib/vcfbreakmulti:
+  - modules/nf-core/vcflib/vcfbreakmulti/**
+  - tests/modules/nf-core/vcflib/vcfbreakmulti/**
 verifybamid/verifybamid2:
   - modules/nf-core/verifybamid/verifybamid2/**
   - tests/modules/nf-core/verifybamid/verifybamid2/**