Added nf-test for gatk4/calibratedragstrmodel (#6321)

Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · 3f42e07 · 3f42e07
1 parent adf8be4
commit 3f42e07
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diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test
@@ -0,0 +1,137 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_CALIBRATEDRAGSTRMODEL"
+    script "../main.nf"
+    process "GATK4_CALIBRATEDRAGSTRMODEL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/calibratedragstrmodel"
+
+    test("test-gatk4-calibratedragstrmodel-bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.dragstr_model[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-gatk4-calibratedragstrmodel-cram") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.dragstr_model[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-gatk4-calibratedragstrmodel-beds") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.dragstr_model[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-gatk4-calibratedragstrmodel-gzipped-beds") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+				input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.dragstr_model[0][1]).readLines()[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap
@@ -0,0 +1,78 @@
+{
+    "test-gatk4-calibratedragstrmodel-bam": {
+        "content": [
+            [
+                "# sample = testN",
+                "# readGroups = 1",
+                "# estimatedOrDefaults = defaults",
+                "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.bam --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",
+                "############################################################################################"
+            ],
+            [
+                "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:22:17.584362"
+    },
+    "test-gatk4-calibratedragstrmodel-cram": {
+        "content": [
+            [
+                "# sample = testN",
+                "# readGroups = 1",
+                "# estimatedOrDefaults = defaults",
+                "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",
+                "############################################################################################"
+            ],
+            [
+                "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:22:30.21551"
+    },
+    "test-gatk4-calibratedragstrmodel-gzipped-beds": {
+        "content": [
+            [
+                "# sample = testN",
+                "# readGroups = 1",
+                "# estimatedOrDefaults = defaults",
+                "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",
+                "############################################################################################"
+            ],
+            [
+                "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:22:53.619871"
+    },
+    "test-gatk4-calibratedragstrmodel-beds": {
+        "content": [
+            [
+                "# sample = testN",
+                "# readGroups = 1",
+                "# estimatedOrDefaults = defaults",
+                "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",
+                "############################################################################################"
+            ],
+            [
+                "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:22:41.938548"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -371,9 +371,6 @@ gappa/examineheattree:
 gatk/indelrealigner:
   - modules/nf-core/gatk/indelrealigner/**
   - tests/modules/nf-core/gatk/indelrealigner/**
-gatk4/calibratedragstrmodel:
-  - modules/nf-core/gatk4/calibratedragstrmodel/**
-  - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
 gatk4/cnnscorevariants:
   - modules/nf-core/gatk4/cnnscorevariants/**
   - tests/modules/nf-core/gatk4/cnnscorevariants/**

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