From 4d682ae6c4762451830a57133dc4db030ee5f27b Mon Sep 17 00:00:00 2001
From: Jo Hausmann <35309108+johausmann@users.noreply.github.com>
Date: Fri, 22 Sep 2023 10:54:37 +0200
Subject: [PATCH 1/3] Update nextflow.config

Add conda.enabled = true
---
 nextflow.config | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 6ed6ce9..1e59245 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,7 +29,10 @@ params.pfam_names_header = "$baseDir/reference/pfam_names.header.txt"
 params.pfam_descriptions_header = "$baseDir/reference/pfam_descriptions.header.txt"
 
 profiles {
-  conda { params.enable_conda = true }
+  conda {
+    params.enable_conda = true
+    conda.enabled = true
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {
     params.cpus = 1

From 307229548387d65444eb26b3cb6fd9d80cf3c46f Mon Sep 17 00:00:00 2001
From: Jo Hausmann <35309108+johausmann@users.noreply.github.com>
Date: Fri, 22 Sep 2023 11:05:46 +0200
Subject: [PATCH 2/3] Update README.md

Added nextflow badge with lastet tested version
Added conda badge
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 1c230f5..437dcc5 100755
--- a/README.md
+++ b/README.md
@@ -1,7 +1,8 @@
 ![CoVigator logo](images/CoVigator_logo_txt_nobg.png "CoVigator logo")
 
 # CoVigator pipeline: variant detection pipeline for Sars-CoV-2
-
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-≤23.04.0-23aa62.svg)](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/)
 [![DOI](https://zenodo.org/badge/374669617.svg)](https://zenodo.org/badge/latestdoi/374669617)
 [![Run tests](https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/actions/workflows/automated_tests.yml/badge.svg?branch=master)](https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/actions/workflows/automated_tests.yml)
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-Nextflow-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.nextflow.io/)

From 172f5d15e7f00ee7481a6ad14ed196be6352a697 Mon Sep 17 00:00:00 2001
From: Jo Hausmann <35309108+johausmann@users.noreply.github.com>
Date: Fri, 22 Sep 2023 11:06:28 +0200
Subject: [PATCH 3/3] Update README.md

Removed old nextflow badge
---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 437dcc5..d6bd394 100755
--- a/README.md
+++ b/README.md
@@ -5,7 +5,6 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![DOI](https://zenodo.org/badge/374669617.svg)](https://zenodo.org/badge/latestdoi/374669617)
 [![Run tests](https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/actions/workflows/automated_tests.yml/badge.svg?branch=master)](https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/actions/workflows/automated_tests.yml)
-[![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-Nextflow-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://www.nextflow.io/)
 [![License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)