From cee8fe33d3ef1a220dee67dac75a32f7c872f63f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20B=C3=A4uerle?=
 <45968370+famosab@users.noreply.github.com>
Date: Wed, 15 May 2024 13:49:01 +0200
Subject: [PATCH] port `gatk4/applyvqsr` to nf-test (#5604)

* port to nf-test update stub

* add more assertions

* update snap

* update tbi test and snap

* change to check for filename
---
 modules/nf-core/gatk4/applyvqsr/main.nf       |   2 +-
 .../applyvqsr/tests/allelspecificity.config   |   5 +
 .../gatk4/applyvqsr/tests/main.nf.test        | 106 ++++++++++++++++++
 .../gatk4/applyvqsr/tests/main.nf.test.snap   |  95 ++++++++++++++++
 .../tests/no-allelspecificity.config          |   5 +
 .../nf-core/gatk4/applyvqsr/tests/tags.yml    |   2 +
 tests/config/pytest_modules.yml               |   3 -
 tests/modules/nf-core/gatk4/applyvqsr/main.nf |  36 ------
 .../nf-core/gatk4/applyvqsr/nextflow.config   |  11 --
 .../modules/nf-core/gatk4/applyvqsr/test.yml  |  19 ----
 10 files changed, 214 insertions(+), 70 deletions(-)
 create mode 100644 modules/nf-core/gatk4/applyvqsr/tests/allelspecificity.config
 create mode 100644 modules/nf-core/gatk4/applyvqsr/tests/main.nf.test
 create mode 100644 modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/gatk4/applyvqsr/tests/no-allelspecificity.config
 create mode 100644 modules/nf-core/gatk4/applyvqsr/tests/tags.yml
 delete mode 100644 tests/modules/nf-core/gatk4/applyvqsr/main.nf
 delete mode 100644 tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
 delete mode 100644 tests/modules/nf-core/gatk4/applyvqsr/test.yml

diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf
index 0506e28185c..047321b8e9e 100644
--- a/modules/nf-core/gatk4/applyvqsr/main.nf
+++ b/modules/nf-core/gatk4/applyvqsr/main.nf
@@ -52,7 +52,7 @@ process GATK4_APPLYVQSR {
     stub:
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gatk4/applyvqsr/tests/allelspecificity.config b/modules/nf-core/gatk4/applyvqsr/tests/allelspecificity.config
new file mode 100644
index 00000000000..ac368bd058b
--- /dev/null
+++ b/modules/nf-core/gatk4/applyvqsr/tests/allelspecificity.config
@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_APPLYVQSR {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS'
+    }
+}
diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test
new file mode 100644
index 00000000000..104eb7f01b4
--- /dev/null
+++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test
@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process GATK4_APPLYVQSR"
+    script "../main.nf"
+    process "GATK4_APPLYVQSR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/applyvqsr"
+
+    test("human - vcf") {
+
+        config "./no-allelspecificity.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - allele-specific") {
+
+        config "./allelspecificity.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions_allelspecific") },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match() }
+            )
+        }
+
+    }
+
+    test("human - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches', checkIfExists: true)
+                        ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap
new file mode 100644
index 00000000000..ad2fe8be65a
--- /dev/null
+++ b/modules/nf-core/gatk4/applyvqsr/tests/main.nf.test.snap
@@ -0,0 +1,95 @@
+{
+    "human - vcf": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:31:50.727658"
+    },
+    "human - vcf - allele-specific": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:29:42.331816"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:00:49.353138"
+    },
+    "human - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:01:24.370421"
+    },
+    "versions_allelspecific": {
+        "content": [
+            [
+                "versions.yml:md5,4a6890d486a62ce6f2edfd2f8961da4f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T13:01:08.104194"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/applyvqsr/tests/no-allelspecificity.config b/modules/nf-core/gatk4/applyvqsr/tests/no-allelspecificity.config
new file mode 100644
index 00000000000..c08c918e1a5
--- /dev/null
+++ b/modules/nf-core/gatk4/applyvqsr/tests/no-allelspecificity.config
@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_APPLYVQSR {
+        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0'
+    }
+}
diff --git a/modules/nf-core/gatk4/applyvqsr/tests/tags.yml b/modules/nf-core/gatk4/applyvqsr/tests/tags.yml
new file mode 100644
index 00000000000..c65706301ad
--- /dev/null
+++ b/modules/nf-core/gatk4/applyvqsr/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/applyvqsr:
+  - "modules/nf-core/gatk4/applyvqsr/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 28e277562f9..982956e9803 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -582,9 +582,6 @@ gatk/realignertargetcreator:
 gatk/unifiedgenotyper:
   - modules/nf-core/gatk/unifiedgenotyper/**
   - tests/modules/nf-core/gatk/unifiedgenotyper/**
-gatk4/applyvqsr:
-  - modules/nf-core/gatk4/applyvqsr/**
-  - tests/modules/nf-core/gatk4/applyvqsr/**
 gatk4/calibratedragstrmodel:
   - modules/nf-core/gatk4/calibratedragstrmodel/**
   - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
diff --git a/tests/modules/nf-core/gatk4/applyvqsr/main.nf b/tests/modules/nf-core/gatk4/applyvqsr/main.nf
deleted file mode 100644
index ea209478555..00000000000
--- a/tests/modules/nf-core/gatk4/applyvqsr/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../../modules/nf-core/gatk4/applyvqsr/main.nf'
-
-workflow test_gatk4_applyvqsr {
-    input = [ [ id:'test'], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_applyvqsr_allele_specific {
-    input = [ [ id:'test'], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
-            ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
-    GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict)
-}
diff --git a/tests/modules/nf-core/gatk4/applyvqsr/nextflow.config b/tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
deleted file mode 100644
index bf943c2337d..00000000000
--- a/tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
+++ /dev/null
@@ -1,11 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    withName: GATK4_APPLYVQSR_NO_ALLELSPECIFICITY {
-        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0'
-    }
-
-    withName: GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY {
-        ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS'
-    }
-}
diff --git a/tests/modules/nf-core/gatk4/applyvqsr/test.yml b/tests/modules/nf-core/gatk4/applyvqsr/test.yml
deleted file mode 100644
index 63e5ceba396..00000000000
--- a/tests/modules/nf-core/gatk4/applyvqsr/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 applyvqsr test_gatk4_applyvqsr
-  command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
-  tags:
-    - gatk4/applyvqsr
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
-  command: nextflow run ./tests/modules/nf-core/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/applyvqsr/nextflow.config
-  tags:
-    - gatk4/applyvqsr
-    - gatk4
-  files:
-    - path: output/gatk4/test.vcf.gz
-    - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml