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cellranger_mkfastq
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BICF
Astrocyte
cellranger_mkfastq
Commits
6b7f1c7f
Commit
6b7f1c7f
authored
Jun 20, 2020
by
Gervaise Henry
🤠
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mkfastq run on high power node, version 2.1.1
parent
6f038019
Pipeline
#7356
passed with stages
in 12 minutes and 13 seconds
Changes
3
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CHANGELOG.md
CHANGELOG.md
+1
-1
workflow/main.nf
workflow/main.nf
+10
-1
workflow/nextflow.config
workflow/nextflow.config
+1
-1
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CHANGELOG.md
View file @
6b7f1c7f
# v2.1.
0
# v2.1.
1
**UserFacing**
*
Check Design File for spaces in name and file contents
*
Update design example, README, and astrocyte.yml with current barcode IDs
...
...
workflow/main.nf
View file @
6b7f1c7f
...
...
@@ -8,6 +8,14 @@ main.nf
*
*/
// ######## #### ###### ########
// ## ## ## ## ## ##
// ## ## ## ## ##
// ######## ## ## ######
// ## ## ## ## ##
// ## ## ## ## ## ##
// ######## #### ###### ##
// Define input variables
params.name = "run"
params.bcl = "${baseDir}/../test_data/simple1/*.tar.gz"
...
...
@@ -24,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.
0
"
pipelineVersion = "2.1.
1
"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
...
...
@@ -142,6 +150,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
input:
...
...
workflow/nextflow.config
View file @
6b7f1c7f
...
...
@@ -47,6 +47,6 @@ manifest {
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.'
mainScript
=
'main.nf'
version
=
'2.1.
0
'
version
=
'2.1.
1
'
nextflowVersion
=
'>=0.31.0'
}
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