Commit 6b7f1c7f authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

mkfastq run on high power node, version 2.1.1

parent 6f038019
Pipeline #7356 passed with stages
in 12 minutes and 13 seconds
# v2.1.0 # v2.1.1
**UserFacing** **UserFacing**
* Check Design File for spaces in name and file contents * Check Design File for spaces in name and file contents
* Update design example, README, and astrocyte.yml with current barcode IDs * Update design example, README, and astrocyte.yml with current barcode IDs
......
...@@ -8,6 +8,14 @@ main.nf ...@@ -8,6 +8,14 @@ main.nf
* *
*/ */
// ######## #### ###### ########
// ## ## ## ## ## ##
// ## ## ## ## ##
// ######## ## ## ######
// ## ## ## ## ##
// ## ## ## ## ## ##
// ######## #### ###### ##
// Define input variables // Define input variables
params.name = "run" params.name = "run"
params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz" params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
...@@ -24,7 +32,7 @@ bclCount = Channel ...@@ -24,7 +32,7 @@ bclCount = Channel
.count() .count()
// Define regular variables // Define regular variables
pipelineVersion = "2.1.0" pipelineVersion = "2.1.1"
name = params.name name = params.name
designLocation = Channel designLocation = Channel
.fromPath(params.designFile) .fromPath(params.designFile)
...@@ -142,6 +150,7 @@ process mkfastq { ...@@ -142,6 +150,7 @@ process mkfastq {
tag "${bcl.simpleName}" tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}" publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.1.0:bcl2fastq/2.19.1' module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input: input:
......
...@@ -47,6 +47,6 @@ manifest { ...@@ -47,6 +47,6 @@ manifest {
homePage = '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 bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.' description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf' mainScript = 'main.nf'
version = '2.1.0' version = '2.1.1'
nextflowVersion = '>=0.31.0' nextflowVersion = '>=0.31.0'
} }
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