Merge pull request #75 from seqeralabs/failed_job

Added parameter to exclude failed tasks from benchmarking report.

Author: FloWuenne

modules/local/benchmark_report/main.nf

@@ -6,6 +6,7 @@ process BENCHMARK_REPORT {
     path run_dumps
     val  groups
     path benchmark_aws_cur_report
+    val  remove_failed_tasks
 
     output:
     path "benchmark_report.html" , emit: benchmark_html
@@ -14,6 +15,8 @@ process BENCHMARK_REPORT {
     script:
     def aws_cost_param = benchmark_aws_cur_report ? "--profile cost -P aws_cost:\$TASK_DIR/${benchmark_aws_cur_report}" : ""
     def benchmark_samplesheet = "benchmark_samplesheet.csv"
+    def failed_tasks = remove_failed_tasks ? "-P remove_failed_tasks:True" : ""
+
     """
     # Set up R environment from renv
     export R_LIBS_USER=/project/renv/library/linux-ubuntu-noble/R-4.4/x86_64-pc-linux-gnu
@@ -33,6 +36,7 @@ process BENCHMARK_REPORT {
     quarto render main_benchmark_report.qmd \\
         -P log_csv:"\$TASK_DIR/"${benchmark_samplesheet} \\
         $aws_cost_param \\
+        $failed_tasks \\
         --output-dir .\\
         --output benchmark_report.html
 

modules/local/benchmark_report/tests/main.nf.test

@@ -0,0 +1,41 @@
+nextflow_process {
+    name "Test Process BENCHMARK_REPORT"
+    script "../main.nf"
+    process "BENCHMARK_REPORT"
+
+        setup {
+            run("SEQERA_RUNS_DUMP") {
+                script "../../seqera_runs_dump/main.nf"
+                process {
+                    """
+                    input[0] = ['id': 'fjV0o6yPbbamB', 'workspace': 'community/showcase', 'group': 'group1']
+                    input[1] = "https://api.tower.nf"
+                    input[2] = ""
+                    input[3] = ""
+                    """
+                }
+            }
+        }
+
+    test("Should run with removing failed tasks") {
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = SEQERA_RUNS_DUMP.out.run_dump.collect{it[1]}
+                input[1] = SEQERA_RUNS_DUMP.out.run_dump.collect{it[0].group}
+                input[2] = []
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert path(process.out.benchmark_html.get(0)).exists()
+            assert path(process.out.versions.get(0)).exists()
+        }
+    }
+}

modules/local/seqera_runs_dump/tests/main.nf.test.snap

@@ -2,7 +2,7 @@
     "Should run without failures": {
         "content": [
             [
-                "service-info.json:md5,75a5b8cded8f0ce9aab2125c0ee89f63",
+                "service-info.json:md5,5738071394871f50948ae77090d4af50",
                 "workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c",
                 "workflow-metadata.json:md5,b37b4faeddf283a2c44cbe4000e4ab6e",
                 "workflow-metrics.json:md5,13a5b5d7447fad4a8baa053d1abf85e5",
@@ -13,8 +13,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "23.10.1"
+            "nextflow": "25.01.0"
         },
-        "timestamp": "2024-11-11T11:53:03.835699"
+        "timestamp": "2025-02-21T15:07:19.112104"
     }
-}
+}

nextflow.config

@@ -28,8 +28,9 @@ params {
     skip_multiqc                 = false
 
     // Benchmark report options
-    generate_benchmark_report                = false
+    generate_benchmark_report    = false
     benchmark_aws_cur_report     = null
+    remove_failed_tasks          = true
 
     // Boilerplate options
     outdir                       = 'results'

nextflow_schema.json

@@ -80,6 +80,11 @@
                     "description": "AWS CUR report from data exports.",
                     "pattern": "^\\S+\\.parquet",
                     "format": "file-path"
+                },
+                "remove_failed_tasks": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-times-circle",
+                    "description": "Remove failed tasks from the benchmark report."
                 }
             },
             "required": ["seqera_api_endpoint"]

subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap

@@ -3,31 +3,46 @@
         "content": [
             [
                 {
+                    "group": [
+                        
+                    ],
                     "id": "2lXd1j7OwZVfxh",
                     "workspace": "community/showcase"
                 },
                 {
+                    "group": [
+                        
+                    ],
                     "id": "38QXz4OfQDpwOV",
                     "workspace": "community/showcase"
                 },
                 {
+                    "group": [
+                        
+                    ],
                     "id": "3iFMo0NtH1Byvy",
                     "workspace": "community/showcase"
                 },
                 {
+                    "group": [
+                        
+                    ],
                     "id": "4Bi5xBK6E2Nbhj",
                     "workspace": "community/showcase"
                 },
                 {
+                    "group": [
+                        
+                    ],
                     "id": "4LWT4uaXDaGcDY",
                     "workspace": "community/showcase"
                 }
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.04.2"
+            "nextflow": "25.01.0"
         },
-        "timestamp": "2024-11-11T11:32:52.476285"
+        "timestamp": "2025-02-26T16:10:24.54507716"
     }
 }

workflows/nf_aggregate/main.nf

@@ -66,9 +66,10 @@ workflow NF_AGGREGATE {
         BENCHMARK_REPORT (
             SEQERA_RUNS_DUMP.out.run_dump.collect{it[1]},
             SEQERA_RUNS_DUMP.out.run_dump.collect{it[0].group},
-            aws_cur_report
+            aws_cur_report,
+            params.remove_failed_tasks
         )
-        ch_versions = ch_versions.mix(BENCHMARK_REPORT.out.versions.first())
+        ch_versions = ch_versions.mix(BENCHMARK_REPORT.out.versions)
     }
 
     //