From 43d6de7118954a9119eb7cdfe7e2c2761fb84ed5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 27 Dec 2019 00:39:04 -0600
Subject: [PATCH] Make bicfbase default container
---
workflow/conf/biohpc.config | 3 +--
workflow/conf/biohpc_local.config | 3 +--
workflow/nextflow.config | 6 +++---
3 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index a8a0c00..d7537db 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -2,13 +2,13 @@ process {
executor = 'slurm'
queue = 'super'
clusterOptions = '--hold'
+ container = 'docker://bicf/bicfbase:1.3'
withLabel:checkDesignFile {
container = 'docker://bicf/python3:1.2'
executor = 'local'
}
withLabel:untarBCL {
- container = 'docker://bicf/bicfbase:1.3'
queue = 'super'
}
withLabel:mkfastq {
@@ -16,7 +16,6 @@ process {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel:countDesign {
- container = 'docker://bicf/bicfbase:1.3'
executor = 'local'
}
withLabel:fastqc {
diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc_local.config
index 5352811..f1e2a31 100644
--- a/workflow/conf/biohpc_local.config
+++ b/workflow/conf/biohpc_local.config
@@ -1,17 +1,16 @@
process {
executor = 'local'
+ container = 'docker://bicf/bicfbase:1.3'
withLabel:checkDesignFile {
container = 'docker://bicf/python3:1.2'
}
withLabel:untarBCL {
- container = 'docker://bicf/bicfbase:1.3'
}
withLabel:mkfastq {
container = 'docker://bicf/cellranger3.1.0:1.0'
}
withLabel:countDesign {
- container = 'docker://bicf/bicfbase:1.3'
}
withLabel:fastqc {
module = ['fastqc/0.11.5', 'parallel']
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index ee8637a..b806753 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -30,14 +30,14 @@ report {
}
tower {
- accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
enabled = true
+ accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
}
manifest {
- homePage = 'https://https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
+ homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf'
version = 'v1.4.0_indev'
- nextflowVersion = '>=19.09.0'
+ nextflowVersion = '>=0.31.0'
}
\ No newline at end of file
--
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