nf-core · ewels · Sep 23, 2023 · Sep 20, 2023 · Sep 21, 2023 · Sep 21, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - ([#2415](https://github.com/nf-core/tools/pull/2415#issuecomment-1709847086)) Add autoMounts for apptainer.
 - Remove `igenomes_base` from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
 - Update Gitpod profile resources to reflect base environment settings.
+- ([#747](https://github.com/nf-core/tools/issues/747)) Add to the template the code to dump the selected pipeline parameters into a json file.
 
 ### Download
 

diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
@@ -64,6 +64,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+  - Parameters used by the pipeline run: `params.json`.
 
 </details>
 

diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -3,6 +3,7 @@
 //
 
 import org.ya
8000
ml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -222,6 +223,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //

diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -120,6 +120,7 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     }
+    NfcoreTemplate.dump_parameters(workflow, params)
     NfcoreTemplate.summary(workflow, params, log)
     if (params.hook_url) {
         NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)