Update vcf_split_bcftools

nf-core · Nov 17, 2024 · 4e0ce65 · 4e0ce65
1 parent a94009a
commit 4e0ce65
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Showing 3 changed files with 80 additions and 10 deletions.
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
@@ -15,15 +15,15 @@ nextflow_workflow {
     tag "bcftools"
     tag "bcftools/split"
 
-    test("Split vcf file") {
+    test("Split multiple vcf file") {
         setup {
             run("BCFTOOLS_MERGE") {
                 script "../../../../modules/nf-core/bcftools/merge/main.nf"
                 process {
                 """
                 input[0] = Channel.of(
                     [
-                        [id: "allSamples"],
+                        [id: "allSamples.batch0"],
                         [file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf", checkIfExist:true),
                         file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s_imputed.bcf", checkIfExist:true),
                         file(params.pipelines_testdata_base_path + "hum_data/individuals/NA20359/NA20359.s_imputed.bcf", checkIfExist:true)],
@@ -43,10 +43,6 @@ nextflow_workflow {
             }
         }
         when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
             workflow {
                 """
                 input[0] = BCFTOOLS_MERGE.out.vcf.join(BCFTOOLS_MERGE.out.tbi)
@@ -74,4 +70,54 @@ nextflow_workflow {
             )
         }
     }
+
+    test("Split one sample vcf file") {
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [id: 'NA12878'],
+                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf", checkIfExist:true),
+                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf.csi", checkIfExist:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.versions,
+                    workflow.out.vcf_tbi.collect{[
+                        it[0],
+                        path(it[1]).getFileName().toString(),
+                        path(it[2]).getFileName().toString()
+                    ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Split no sample vcf file") {
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [id: 'dbsnp_146.hg38'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExist:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExist:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz")
+                }
+            )
+        }
+    }
 }
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
@@ -1,5 +1,26 @@
 {
-    "Split vcf file": {
+    "Split one sample vcf file": {
+        "content": [
+            [
+                "versions.yml:md5,6c3351d97e3a99f7a7a3231fc49f92e2"
+            ],
+            [
+                [
+                    {
+                        "id": "NA12878"
+                    },
+                    "NA12878.vcf.gz",
+                    "NA12878.vcf.gz.tbi"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T14:06:59.745818945"
+    },
+    "Split multiple vcf file": {
         "content": [
             [
                 "versions.yml:md5,6c3351d97e3a99f7a7a3231fc49f92e2"
@@ -34,9 +55,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T14:13:06.801872176"
+        "timestamp": "2024-11-11T14:42:48.076610625"
     }
-}
+}
diff --git a/subworkflows/local/vcf_split_bcftools/tests/nextflow.config b/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
@@ -1,7 +1,10 @@
 process {
+    resourceLimits = [cpus: 2, memory: '2.GB']
+
     withName: BCFTOOLS_MERGE {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }
+
     withName: BCFTOOLS_PLUGINSPLIT {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }