add enable_conda to remove warnings on runtime

CDCgov · Mar 18, 2024 · 34c9861 · 34c9861
1 parent b713db8
commit 34c9861
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/conf/test_params.config b/conf/test_params.config
@@ -57,6 +57,7 @@ params {
         docker_container                = 'staphb/tostadas:latest'
         docker_container_vadr           = 'staphb/vadr:latest'
         docker_container_bakta          = 'quay.io/biocontainers/bakta:1.8.2--pyhdfd78af_0'
+        enable_conda                    = false
         /*
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 ANNOTATION SUBWORKFLOW 

diff --git a/nextflow.config b/nextflow.config
@@ -73,9 +73,7 @@ params {
     docker_container       = 'staphb/tostadas:latest'
     docker_container_vadr  = 'staphb/vadr:latest'
     scicomp                = false
-    run_conda              = false
-    run_docker             = false
-    run_singularity        = false
+    enable_conda           = false
 
     // cleanup subworkflow
     cleanup                = false
@@ -166,7 +164,7 @@ profiles {
 
     // run docker + specify settings 
     conda {
-        enable_conda           = true
+        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -181,7 +179,7 @@ profiles {
         params.run_singularity   = false 
     }
     docker {
-        enable_conda           = false
+        params.enable_conda    = false
         docker.enabled         = true
         docker.userEmulation   = true
         singularity.enabled    = false
@@ -202,10 +200,10 @@ profiles {
         }
     }
     singularity {
+        params.enable_conda    = false
         singularity.enabled    = true
         singularity.autoMounts = true
         docker.enabled         = false
-        enable_conda           = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false