diff --git a/nextflow.config b/nextflow.config index 69f0eec..146d605 100644 --- a/nextflow.config +++ b/nextflow.config @@ -115,46 +115,39 @@ profiles { test { // default workflow params.sra_accessions = ["SRR11725329", "SRR13643280", "SRR14436834", "SRR14634837", "SRR7738178", "SRR7889058"] - params.publish_dir_mode = "link" } test0 { // default workflow while skipping extras params.sra_accessions = ["SRR11725329", "SRR13643280"] params.skip_extras = true - params.publish_dir_mode = "link" } test1 { // turning on current datasets params.sra_accessions = ["SRR11725329", "SRR13643280", "SRR14436834", "SRR14634837", "SRR7738178", "SRR7889058"] params.current_datasets = true - params.publish_dir_mode = "link" } test2 { // phylogenetic analysis params.sra_accessions = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ] params.msa = true - params.publish_dir_mode = "link" } test3 { // phylogenetic analysis without extras params.sra_accessions = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ] params.msa = true params.skip_extras = true - params.publish_dir_mode = "link" } test4 { // phylogenetic analysis with current datasets params.sra_accessions = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ] params.msa = true params.current_datasets = true - params.publish_dir_mode = "link" } test5 { // phylogenetic analysis and exclude fastani top hit params.sra_accessions = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ] params.msa = true params.exclude_top_hit = true - params.publish_dir_mode = "link" } test6 { // phylogenetic analysis with roary and exclude fastani top hit @@ -162,7 +155,6 @@ profiles { params.msa = true params.exclude_top_hit = true params.aligner = 'roary' - params.publish_dir_mode = "link" } uphl { includeConfig './conf/UPHL.config' @@ -172,13 +164,11 @@ profiles { params.sra_accessions = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ] params.msa = true params.annotator = 'prokka' - params.publish_dir_mode = "link" } test8 { // phylogenetic analysis with genome accessions params.genome_accessions = ["GCF_900475035.1", "GCF_022869605.1", "GCF_002055535.1", "GCF_004028355.1" ] params.msa = true - params.publish_dir_mode = "link" } }