From 275173103e949233ffd154a647f31c2524979c8b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 26 Dec 2019 23:25:04 -0600
Subject: [PATCH] Remove modules and queues from nf
---
workflow/main.nf | 9 ---------
1 file changed, 9 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 9d5a92d..1f8219a 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -36,7 +36,6 @@ references = params.references
process checkDesignFile {
tag "${name}"
- module 'python/3.6.1-2-anaconda'
input:
file designLocation
@@ -62,7 +61,6 @@ process checkDesignFile {
process untarBCL {
tag "${tar}"
- module 'pigz/2.4'
input:
file tar from tarList
@@ -83,9 +81,7 @@ process untarBCL {
process mkfastq {
tag "${bcl.baseName}"
- queue '128GB,256GB,256GBv1,384GB'
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
- module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input:
each bcl from bclPaths.collect()
@@ -134,8 +130,6 @@ if (bclCount.value == 1) {
process fastqc {
tag "${bclName}"
- queue 'super'
- module 'fastqc/0.11.5:parallel'
input:
file fastqPaths
@@ -158,7 +152,6 @@ process fastqc {
process versions {
tag "${name}"
- module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
@@ -182,9 +175,7 @@ process versions {
process multiqc {
tag "${name}"
- queue 'super'
publishDir "${outDir}/${task.process}/${name}", mode: 'copy', pattern: "{multiqc*}"
- module 'multiqc/1.7'
input:
file bqc name "bqc/?/*" from bqcPaths.collect()
--
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