From e349d9968f11af098f1f9c32ee0df2fcef525dbf Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 21 Jul 2022 11:05:57 -0500
Subject: [PATCH] Add mamba to Nextflow config

---
 dot_nextflow/config.tmpl | 96 +---------------------------------------
 1 file changed, 2 insertions(+), 94 deletions(-)

diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl
index f4bc612..12db9cf 100644
--- a/dot_nextflow/config.tmpl
+++ b/dot_nextflow/config.tmpl
@@ -4,99 +4,7 @@ tower {
   accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}'
 }
 {{ end }}
-profiles {
-  aahz {
-    params {
-      config_profile_description = 'KSU VDL Molecular NGS Big Server profile'
-      config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
-      config_profile_url         = null
 
-      max_memory = 745.GB
-      max_cpus   = 78
-      max_time   = 7.d
-    }
-    singularity {
-      enabled      = true
-      autoMounts   = true
-      envWhitelist = 'NCBI_API_KEY'
-    }
-    process {
-      executor = 'local'
-    }
-  }
-  atlas {
-    params {
-      config_profile_description = 'Mississippi State University Atlas Cluster profile'
-      config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
-      config_profile_url         = 'https://www.hpc.msstate.edu/computing/atlas/'
-
-      max_memory = 1539.GB
-      max_cpus   = 24
-      max_time   = 14.d
-    }
-    singularity {
-      enabled      = true
-      autoMounts   = true
-      envWhitelist = 'NCBI_API_KEY'
-    }
-    process {
-      scratch        = true
-      executor       = 'slurm'
-      clusterOptions = '--account=fabadru'
-
-      withLabel: process_high_memory {
-        queue = 'bigmem'
-      }
-    }
-  }
-  ceres {
-    params {
-      config_profile_description = 'USDA ARS SCInet Ceres Cluster profile'
-      config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
-      config_profile_url         = 'https://scinet.usda.gov/guide/ceres/#partitions-or-queues'
-
-      max_memory = 768.GB
-      max_cpus   = 40
-      max_time   = 1000.h
-    }
-    singularity {
-      enabled      = true
-      autoMounts   = true
-      envWhitelist = 'NCBI_API_KEY'
-    }
-    process {
-      scratch  = true
-      executor = 'slurm'
-      queue    = 'short'
-
-      withLabel: process_high_memory {
-        queue = 'mem'
-      }
-      withLabel: process_long {
-        queue = 'long'
-      }
-      withLabel: process_medium {
-        queue = 'medium'
-      }
-    }
-  }
-  tananda {
-    params {
-      config_profile_description = 'KSU VDL Molecular NGS Desktop profile'
-      config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
-      config_profile_url         = null
-
-      max_memory = 14.GB
-      max_cpus   = 12
-      max_time   = 4.h
-    }
-    docker {
-      enabled       = true
-      userEmulation = true
-      envWhitelist  = 'NCBI_API_KEY'
-    }
-    process {
-      executor = 'local'
-    }
-  }
+conda {
+  useMamba = true
 }