diff --git a/modules/local/download_proteins.nf b/modules/local/download_proteins.nf index b1172617..2736463d 100644 --- a/modules/local/download_proteins.nf +++ b/modules/local/download_proteins.nf @@ -9,6 +9,8 @@ process DOWNLOAD_PROTEINS { 'biocontainers/biopython:1.78' }" input: + env NCBI_EMAIL + env NCBI_KEY val microbiome_ids path microbiome_files diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test index 3a2f9993..3265a49d 100644 --- a/tests/pipeline/test_taxa_specific_assembly.nf.test +++ b/tests/pipeline/test_taxa_specific_assembly.nf.test @@ -10,8 +10,8 @@ nextflow_pipeline { when { params { outdir = "$outputDir" - ncbi_email = "\\\${NCBI_EMAIL}" - ncbi_key = '\\\${NCBI_KEY}' + ncbi_email = "\${NCBI_EMAIL}" + ncbi_key = '\${NCBI_KEY}' } }