Merge pull request #1301 from maxulysse/nfprov

FIX: nf-prov usage

CHANGELOG.md

@@ -22,7 +22,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - [#1277](https://github.com/nf-core/sarek/pull/1277) - Fix null value issue for Mutect2 joint calling
-- [#1287](https://github.com/nf-core/sarek/pull/1287) - Adding label `process_single` to local modules.
+- [#1287](https://github.com/nf-core/sarek/pull/1287) - Adding label `process_single` to local modules
+- [#1301](https://github.com/nf-core/sarek/pull/1301) - Fix nf-prov usage
 
 ### Dependencies
 

docs/output.md

@@ -55,6 +55,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Variant annotation](#variant-annotation)
   - [snpEff](#snpeff)
   - [VEP](#vep)
+  - [BCFtools annotate](#bcftools-annotate)
 - [Quality control and reporting](#quality-control-and-reporting)
   - [Quality control](#quality-control)
     - [FastQC](#fastqc)
@@ -1141,10 +1142,9 @@ Results generated by MultiQC collect pipeline QC from supported tools e.g. FastQ
 <summary>Output files</summary>
 
 - `pipeline_info/`
-  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
+  - Reports generated by Nextflow: `execution_report_<timestamp>.html`, `execution_timeline_<timestamp>.html`, `execution_trace_<timestamp>.txt`, `pipeline_dag_<timestamp>.dot`/`pipeline_dag_<timestamp>.svg` and `manifest_<timestamp>.bco.json`.
   - 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`.
+  - Parameters used by the pipeline run: `params_<timestamp>.json`.
 
 </details>
 

nextflow.config

@@ -337,7 +337,11 @@ dag {
 }
 prov {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
+    formats {
+        bco {
+            file = "${params.outdir}/pipeline_info/manifest_${trace_timestamp}.bco.json"
+        }
+    }
 }
 
 manifest {