Update solutions

Author: pinin4fjords

nf4-science/genomics/solutions/modules/modules/gatk/haplotypecaller/main.nf renamed to nf4-science/genomics/solutions/modules/gatk/haplotypecaller/main.nf

@@ -0,0 +1,111 @@
+nextflow_process {
+
+    name "Test Process GATK_HAPLOTYPECALLER"
+    script "../main.nf"
+    process "GATK_HAPLOTYPECALLER"
+
+    test("Should call son's halotype correctly") {
+
+        setup {
+            run("SAMTOOLS_INDEX") {
+                script "../../../samtools/index/main.nf"
+                process {
+                    """
+                    input[0] =  file("${projectDir}/data/bam/reads_son.bam")
+                    """
+                }
+            }
+        }
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = SAMTOOLS_INDEX.out
+                input[1] = file("${projectDir}/data/ref/ref.fasta")
+                input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+                input[3] = file("${projectDir}/data/ref/ref.dict")
+                input[4] = file("${projectDir}/data/ref/intervals.bed")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out[0][0]).readLines().contains('#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	reads_son')
+            assert path(process.out[0][0]).readLines().contains('20_10037292_10066351	3277	.	G	<NON_REF>	.	.	END=3282	GT:DP:GQ:MIN_DP:PL	0/0:25:72:24:0,72,719')
+        }
+
+    }
+
+    test("Should call mother's halotype correctly") {
+
+        setup {
+            run("SAMTOOLS_INDEX") {
+                script "../../../samtools/index/main.nf"
+                process {
+                    """
+                    input[0] =  file("${projectDir}/data/bam/reads_mother.bam")
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = SAMTOOLS_INDEX.out
+                input[1] = file("${projectDir}/data/ref/ref.fasta")
+                input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+                input[3] = file("${projectDir}/data/ref/ref.dict")
+                input[4] = file("${projectDir}/data/ref/intervals.bed")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out[0][0]).readLines().contains('#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	reads_mother')
+            assert path(process.out[0][0]).readLines().contains('20_10037292_10066351	3277	.	G	<NON_REF>	.	.	END=3278	GT:DP:GQ:MIN_DP:PL	0/0:38:99:37:0,102,1530')
+        }
+    }
+
+    test("Should call father's halotype correctly") {
+
+        setup {
+            run("SAMTOOLS_INDEX") {
+                script "../../../samtools/index/main.nf"
+                process {
+                    """
+                    input[0] =  file("${projectDir}/data/bam/reads_father.bam")
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = SAMTOOLS_INDEX.out
+                input[1] = file("${projectDir}/data/ref/ref.fasta")
+                input[2] = file("${projectDir}/data/ref/ref.fasta.fai")
+                input[3] = file("${projectDir}/data/ref/ref.dict")
+                input[4] = file("${projectDir}/data/ref/intervals.bed")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out[0][0]).readLines().contains('#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	reads_father')
+            assert path(process.out[0][0]).readLines().contains('20_10037292_10066351	3277	.	G	<NON_REF>	.	.	END=3281	GT:DP:GQ:MIN_DP:PL	0/0:44:99:42:0,120,1800')
+        }
+    }
+}

nf4-science/genomics/solutions/modules/gatk/haplotypecaller/tests/main.nf.test

@@ -0,0 +1,25 @@
+{
+    "Should call son's halotype correctly": {
+        "content": [
+            {
+                "0": [
+                    "reads_son.bam.g.vcf:md5,069316cdd4328542ffc6ae247b1dac39"
+                ],
+                "1": [
+                    "reads_son.bam.g.vcf.idx:md5,dc36c18f2afdc546f41e68b2687e9334"
+                ],
+                "idx": [
+                    "reads_son.bam.g.vcf.idx:md5,dc36c18f2afdc546f41e68b2687e9334"
+                ],
+                "vcf": [
+                    "reads_son.bam.g.vcf:md5,069316cdd4328542ffc6ae247b1dac39"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2025-03-04T09:26:58.537420116"
+    }
+}