Merge pull request #3296 from mirpedrol/fix-nextflow-language-server-…

…template Template: Remove `def` from `nextflow.config` and add `trace_report_suffix` param
nf-core · Nov 26, 2024 · 6a6de1d · 6a6de1d
2 parents 4e4bbaa + d56c87c
commit 6a6de1d
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Showing 4 changed files with 14 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - fix workflow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235))
 - Add resource limits to Gitpod profile([#3255](https://github.com/nf-core/tools/pull/3255))
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
+- Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
 
 ### Download
 

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -52,6 +52,7 @@ params {
     version                      = false
     {%- if test_config %}
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     {%- if nf_core_configs -%}
     // Config options
@@ -249,22 +250,21 @@ set -C # No clobber - prevent output redirection from overwriting files.
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 
 manifest {

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -229,7 +229,13 @@
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
-                }{% endif %}
+                }{% endif %},
+                "trace_report_suffix": {
+                    "type": "string",
+                    "fa_icon": "far calendar",
+                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
+                    "hidden": true
+                }
             }
         }
     },

diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
@@ -96,6 +96,7 @@ def _update_validation_plugin_from_config(self) -> None:
                 conf.get("validation.help.shortParameter", "help"),
                 conf.get("validation.help.fullParameter", "helpFull"),
                 conf.get("validation.help.showHiddenParameter", "showHidden"),
+                "trace_report_suffix",  # report suffix should be ignored by default as it is a Java Date object
             ]  # Help parameter should be ignored by default
             ignored_params_config_str = conf.get("validation.defaultIgnoreParams", "")
             ignored_params_config = [