Merge pull request #53 from TRON-Bioinformatics/52_restore_conda_comp…

…atibility

52 restore conda compatibility with newer nextflow versions

README.md

@@ -1,10 +1,10 @@
 ![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/)
 [![License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
 
 

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