From e83f8c5f0e7020d69649d5d2ad19f79e9b2302b7 Mon Sep 17 00:00:00 2001 From: Anthony Underwood Date: Fri, 18 Jun 2021 14:53:55 +0100 Subject: [PATCH 1/2] Add zenodo badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 639d627..0691242 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/bactmap/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bactmap/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/bactmap/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bactmap/actions?query=workflow%3A%22nf-core+linting%22) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/bactmap/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Cite with Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.4743799.svg)](https://doi.org/10.5281/zenodo.4743799) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) From 9fbab1e92d3cbb0b2237c9afca113fe932462110 Mon Sep 17 00:00:00 2001 From: Adam Dinan Date: Mon, 20 Mar 2023 14:30:03 +0000 Subject: [PATCH 2/2] Run MULTIQC only if trimming enabled --- workflows/bactmap.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/bactmap.nf b/workflows/bactmap.nf index ef758d3..e13ed73 100644 --- a/workflows/bactmap.nf +++ b/workflows/bactmap.nf @@ -222,7 +222,8 @@ workflow BACTMAP { workflow_summary = WorkflowBactmap.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - MULTIQC ( + if (params.trim){ + MULTIQC ( ch_multiqc_config, ch_multiqc_custom_config.collect().ifEmpty([]), GET_SOFTWARE_VERSIONS.out.yaml.collect(), @@ -232,6 +233,7 @@ workflow BACTMAP { VARIANTS_BCFTOOLS.out.stats.collect{it[1]}.ifEmpty([]) ) multiqc_report = MULTIQC.out.report.toList() + } } /*