From e762ce1914d938f307ec3f8de108499bfd7799b2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 21 Feb 2020 11:01:56 -0600
Subject: [PATCH] Remove redundant nextflow.config
---
nextflow.config | 52 ----------------------------------------
workflow/nextflow.config | 49 ++++++++++++++++++++++++++++++++++++-
2 files changed, 48 insertions(+), 53 deletions(-)
delete mode 100644 nextflow.config
diff --git a/nextflow.config b/nextflow.config
deleted file mode 100644
index f1a8650..0000000
--- a/nextflow.config
+++ /dev/null
@@ -1,52 +0,0 @@
-profiles {
- biohpc {
- includeConfig 'conf/biohpc.config'
- }
- local {
- includeConfig 'conf/biohpc_local.config'
- }
- cluster {
- includeConfig 'conf/biohpc_cluster.config'
- }
- aws {
- includeConfig 'conf/aws.config'
- }
- ondemand {
- includeConfig 'conf/aws_ondemand.config'
- }
- spot {
- includeConfig 'conf/aws_spot.config'
- }
- awsUserDefined {
- includeConfig 'conf/aws_user.config'
- }
-}
-
-trace {
- enabled = true
- file = 'pipeline_trace.txt'
- fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
-}
-
-timeline {
- enabled = true
- file = 'timeline.html'
-}
-
-report {
- enabled = true
- file = 'report.html'
-}
-
-tower {
- accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
- enabled = true
-}
-
-manifest {
- homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
- description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
- mainScript = 'main.nf'
- version = 'v1.2.1_indev'
- nextflowVersion = '>=0.31.0'
-}
\ No newline at end of file
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 30e47ea..f1a8650 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,5 +1,52 @@
profiles {
- standard {
+ biohpc {
includeConfig 'conf/biohpc.config'
}
+ local {
+ includeConfig 'conf/biohpc_local.config'
+ }
+ cluster {
+ includeConfig 'conf/biohpc_cluster.config'
+ }
+ aws {
+ includeConfig 'conf/aws.config'
+ }
+ ondemand {
+ includeConfig 'conf/aws_ondemand.config'
+ }
+ spot {
+ includeConfig 'conf/aws_spot.config'
+ }
+ awsUserDefined {
+ includeConfig 'conf/aws_user.config'
+ }
+}
+
+trace {
+ enabled = true
+ file = 'pipeline_trace.txt'
+ fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}
+
+timeline {
+ enabled = true
+ file = 'timeline.html'
+}
+
+report {
+ enabled = true
+ file = 'report.html'
+}
+
+tower {
+ accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
+ enabled = true
}
+
+manifest {
+ homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
+ description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
+ mainScript = 'main.nf'
+ version = 'v1.2.1_indev'
+ nextflowVersion = '>=0.31.0'
+}
\ No newline at end of file
--
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