Make use of threads

Author: bagnacan

modules/nf-core/delly/call/main.nf

@@ -37,6 +37,7 @@ process DELLY_CALL {
     delly \\
         call \\
         ${args} \\
+        --threads ${task.cpus} \\
         ${bcf_output} \\
         --genome ${fasta} \\
         ${genotype} \\

modules/nf-core/delly/call/tests/cpus.config

@@ -0,0 +1,5 @@
+process {
+    withName: "DELLY_CALL" {
+        cpus = 2
+    }
+}

modules/nf-core/delly/call/tests/main.nf.test

@@ -45,6 +45,41 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai - cpus") {
+
+        config "./cpus.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
+                    [],
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [ id:'fasta' ],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
+                ]
+                input[2] = [
+                    [ id:'fai' ],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
     test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
 
         when {

modules/nf-core/delly/call/tests/main.nf.test.snap

@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,d4da44c1455810fe699cc63c12b25ff4"
                     ]
                 ],
                 "csi": [
@@ -61,7 +61,41 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:51:33.931579498",
+        "timestamp": "2026-03-28T00:22:24.774120386",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai - cpus": {
+        "content": [
+            {
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d4da44c1455810fe699cc63c12b25ff4"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                    ]
+                ],
+                "versions_delly": [
+                    [
+                        "DELLY_CALL",
+                        "delly",
+                        "1.7.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-28T00:21:15.58823983",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -75,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,d4da44c1455810fe699cc63c12b25ff4"
                     ]
                 ],
                 "csi": [
@@ -95,7 +129,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:50:57.395295355",
+        "timestamp": "2026-03-28T00:21:38.783461969",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -109,7 +143,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,d4da44c1455810fe699cc63c12b25ff4"
                     ]
                 ],
                 "csi": [
@@ -129,7 +163,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:51:14.902129068",
+        "timestamp": "2026-03-28T00:22:01.408245362",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -143,7 +177,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,e030fce4d07043b1b1101238394f0b58"
+                        "test.vcf.gz:md5,0a81ce46f60c9216891e6470ef6f9890"
                     ]
                 ],
                 "csi": [
@@ -163,7 +197,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:50:35.147896323",
+        "timestamp": "2026-03-28T00:20:44.631319255",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"