removed link since it wasn't doing anything

UPHL-BioNGS · Jan 18, 2025 · fdd489d · fdd489d
1 parent f025608
commit fdd489d
Showing 1 changed file with 0 additions and 10 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -115,54 +115,46 @@ 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
     params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
     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"
     }
 
 }