fix(ci): unblock stacked PR checks

Author: edmundmiller

.nf-core.yml

@@ -0,0 +1,35 @@
+lint:
+  base_config: false
+  files_exist: false
+  files_unchanged: false
+  modules_config: false
+  multiqc_config: false
+  nextflow_config:
+    - custom_config
+    - manifest.homePage
+    - manifest.name
+    - process.cpus
+    - process.memory
+    - process.time
+  pipeline_name_conventions: false
+  schema_lint: false
+  template_strings:
+    - bin/benchmark_report_template.html
+    - assets/AGENTS.md
+  nf_test_content:
+    - tests/nextflow.config
+nf_core_version: 3.3.1
+repository_type: pipeline
+template:
+  author: SciDev Team
+  description: Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.
+  force: false
+  is_nfcore: false
+  name: nf-aggregate
+  org: seqeralabs
+  outdir: .
+  skip_features:
+    - ci
+    - igenomes
+    - nf_core_configs
+  version: 0.7.0

.prettierignore

@@ -7,3 +7,7 @@ testing/
 testing*
 *.pyc
 bin/
+**/AGENTS.md
+docs/DESIGN.md
+renovate.json
+workflows/nf_aggregate/assets/log_dirs/

main.nf

@@ -13,17 +13,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { NF_AGGREGATE         } from './workflows/nf_aggregate'
-include {
-    checkCondaChannels ;
-    dumpParametersToJSON ;
-    getWorkflowVersion
-} from 'plugin/nf-core-utils'
-include {
-    paramsSummaryLog ;
-    samplesheetToList ;
-    validateParameters
-} from 'plugin/nf-schema'
+include { NF_AGGREGATE } from './workflows/nf_aggregate'
+include { checkCondaChannels; dumpParametersToJSON; getWorkflowVersion } from 'plugin/nf-core-utils'
+include { paramsSummaryLog; samplesheetToList; validateParameters } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

renovate.json

@@ -1,4 +1,4 @@
 {
-  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
-  "baseBranches": ["dev"]
+    "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+    "baseBranches": ["dev"]
 }

workflows/nf_aggregate/main.nf

@@ -32,8 +32,10 @@ workflow NF_AGGREGATE {
     if (!params.generate_benchmark_report) {
         ch_split.api.count().subscribe { n ->
             if (n > 0) {
-                log.warn "Found ${n} API run(s) but --generate_benchmark_report is not enabled. " +
-                         "API runs will not produce any output. Enable --generate_benchmark_report to process them."
+                log.warn(
+                    "Found ${n} API run(s) but --generate_benchmark_report is not enabled. " +
+                    "API runs will not produce any output. Enable --generate_benchmark_report to process them."
+                )
             }
         }
     }