diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 61f767d..9983779 100644 --- a/.github/workflows/main.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 02b1cc8..5987ffc 100644 --- a/CHANGELOG.md +++ b/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. diff --git a/bin/vcfparser.pyc b/bin/vcfparser.pyc index b370e4f..61a1c29 100644 Binary files a/bin/vcfparser.pyc and b/bin/vcfparser.pyc differ diff --git a/nextflow.config b/nextflow.config index ad607dc..7597952 100644 --- a/nextflow.config +++ b/nextflow.config @@ -264,20 +264,29 @@ 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' @@ -285,8 +294,12 @@ manifest { 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 'nf-prov@1.2.2' // Provenance reports for pipeline runs } // Load modules.config for DSL2 module specific options