feat: Add failed tasks param

Author: edmundmiller

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
 

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"]

workflows/nf_aggregate/main.nf

@@ -66,7 +66,8 @@ 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())
     }