From 1baad703c255c6f44b0c56ea320e5c432e841910 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 21 Feb 2020 10:58:14 -0600
Subject: [PATCH] Add profiles to nextflow.config
---
nextflow.config | 51 +++++++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 49 insertions(+), 2 deletions(-)
diff --git a/nextflow.config b/nextflow.config
index 2877704..f1a8650 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,5 +1,52 @@
profiles {
- standard {
- includeConfig 'workflow/conf/biohpc.config'
+ 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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