From 63b69db801a772ab6dda64b7f8a91eb2dfca35e3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 20:33:58 -0500
Subject: [PATCH] Fix config filenames

---
 workflow/conf/biohpc.config | 53 -------------------------------------
 workflow/nextflow.config    |  4 +--
 2 files changed, 2 insertions(+), 55 deletions(-)
 delete mode 100755 workflow/conf/biohpc.config

diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
deleted file mode 100755
index 7304219..0000000
--- a/workflow/conf/biohpc.config
+++ /dev/null
@@ -1,53 +0,0 @@
-params {
-  // Reference file paths on BioHPC
-  genomes {
-    'GRCh38-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38_and_mm10-3.1.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'ercc92-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-  }
-  // Chemistry mapping parameter
-  chemistry {
-    'auto' {
-      param = 'auto'
-    }
-    '3GEXv1' {
-      param = 'SC3Pv1'
-    }
-   '3GEXv2' {
-      param = 'SC3Pv2'
-    }
-   '3GEXv3' {
-      param = 'SC3Pv3'
-    }
-   '5GEX' {
-      param = 'fiveprime'
-    }
-  }
-}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 94688ff..527b3ca 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,8 +1,8 @@
 profiles {
-  biohpc.local {
+  biohpc_local {
     includeConfig 'conf/biohpc_local.config'
   }
-  biohpc.cluster {
+  biohpc_cluster {
     includeConfig 'conf/biohpc_cluster.config'
   }
   aws {
-- 
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