fix rocrate

seqeralabs · Feb 26, 2025 · e8cc1fe · e8cc1fe
1 parent 832a12c
commit e8cc1fe
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Showing 3 changed files with 154 additions and 49 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -41,7 +41,6 @@ params {
     show_hidden                  = false
     version                      = false
     modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     // Schema validation default options
@@ -313,7 +312,7 @@ manifest {
     homePage        = 'https://github.com/seqeralabs/nf-aggregate'
     description     = """Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform."""
     mainScript      = 'main.nf'
-    defaultBranch   = 'master'
+    defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
     version         = '0.5.0'
     doi             = ''
@@ -325,7 +324,6 @@ plugins {
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
     help {
         enabled = true

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -31,6 +31,64 @@
                 }
             }
         },
+        "pipeline_options": {
+            "title": "Pipeline-specific options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Generic options for the pipeline.",
+            "help_text": "Generic options for the pipeline.",
+            "properties": {
+                "seqera_api_endpoint": {
+                    "type": "string",
+                    "default": "https://api.cloud.seqera.io",
+                    "description": "Seqera Platform API endpoint URL.",
+                    "fa_icon": "fas fa-question-circle"
+                },
+                "seqera_cli_extra_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to the Seqera Platform CLI command in addition to defaults defined by the pipeline.",
+                    "fa_icon": "fas fa-plus"
+                },
+                "java_truststore_path": {
+                    "type": "string",
+                    "description": "Path to custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
+                "java_truststore_password": {
+                    "type": "string",
+                    "description": "Password for custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
+                "skip_run_gantt": {
+                    "type": "boolean",
+                    "description": "Skip GANTT chart creation for each run.",
+                    "fa_icon": "fas fa-fast-forward"
+                },
+                "skip_multiqc": {
+                    "type": "boolean",
+                    "description": "Skip MultiQC.",
+                    "fa_icon": "fas fa-fast-forward"
+                },
+                "generate_benchmark_report": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-tachometer-alt",
+                    "description": "Compile a benchmarking report for Seqera Platform runs."
+                },
+                "benchmark_aws_cur_report": {
+                    "type": "string",
+                    "fa_icon": "fas fa-dollar-sign",
+                    "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"]
+        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -119,13 +177,6 @@
                     "hidden": true,
                     "fa_icon": "fas fa-clone"
                 },
-                "pipelines_testdata_base_path": {
-                    "type": "string",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
-                    "hidden": true
-                },
                 "trace_report_suffix": {
                     "type": "string",
                     "fa_icon": "far calendar",