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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