add nf-prov

.github/workflows/main.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - dev
-      - 14-cicd-test-integration
+      - master
   pull_request:
   release:
     types: [published]
@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ["22.10.6"]
+        nxf_ver: ["23.10.3"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3

CHANGELOG.md

@@ -3,6 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+**Full Changelog**: https://github.com/ghga-de/nf-snvcalling/compare/v1.0...v2.0.0
+## v1.0dev - [date]
+
+Initial release of ghga-de/nf-snvcalling, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v2.0.0 - 24.06.2024
 
 ### `Added`
@@ -52,15 +65,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * re-arrange resources for dkfz cluster by @kubranarci in https://github.com/ghga-de/nf-snvcalling/pull/34
 * 35 raw vcf is not sorted by @kubranarci in https://github.com/ghga-de/nf-snvcalling/pull/36
 
-**Full Changelog**: https://github.com/ghga-de/nf-snvcalling/compare/v1.0...v2.0.0
-## v1.0dev - [date]
 
-Initial release of ghga-de/nf-snvcalling, created with the [nf-core](https://nf-co.re/) template.
+## v2.0.1 - 09.10.2024
 
 ### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`
+ - nf-prov plugin is added.

nextflow.config

@@ -264,29 +264,42 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.tracedir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.tracedir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.tracedir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.tracedir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
+prov 
+    {
+    enabled = true
+    formats {
+        bco {
+            file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
+        }
+    }
+    }
 
 manifest {
     name            = 'nf-snvcalling'
     author          = 'Kuebra Narci [email protected]'
     homePage        = 'https://github.com/kubranarci/nf-snvcalling'
     description     = 'ODCF SNV Calling pipeline'
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=21.10.3'
-    version         = '1.0dev'
+    nextflowVersion = '!>=23.10.3'
+    version         = '2.0.1'
+}
+// Nextflow plugins
+plugins {
+    id '[email protected]'       // Provenance reports for pipeline runs
 }
 
 // Load modules.config for DSL2 module specific options