From cbe97552961fdc5f1e49cd1091233c46c0abc673 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 20 Jul 2022 08:00:00 +0000 Subject: [PATCH] simplify multiqc_config channel --- CHANGELOG.md | 1 + workflows/sarek.nf | 9 ++++----- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 106c24c75..c8317bc9c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -143,6 +143,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic - [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks - [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files +- [#666](https://github.com/nf-core/sarek/pull/666) - Simplify multiqc config channel input ### Deprecated diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 82a3d8fdb..f1f8e790c 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -977,13 +977,12 @@ workflow SAREK { ch_workflow_summary = Channel.value(workflow_summary) ch_multiqc_files = Channel.empty().mix(ch_version_yaml, - Channel.from(ch_multiqc_config), - ch_multiqc_custom_config.collect().ifEmpty([]), ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'), - ch_reports.collect() - ) + ch_reports.collect()) - MULTIQC(ch_multiqc_files.collect(), ch_multiqc_config) + ch_multiqc_configs = Channel.from(ch_multiqc_config).mix(ch_multiqc_custom_config).ifEmpty([]) + + MULTIQC(ch_multiqc_files.collect(), ch_multiqc_configs.collect()) multiqc_report = MULTIQC.out.report.toList() } }