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Commit 27127abe authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge branch 'develop' into 'master'

Develop

See merge request !18
parents 6ef47c9a d429a220
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Tags
4 merge requests!29Develop,!20Master,!19Master,!18Develop
Pipeline #3203 passed with stage
in 22 minutes and 56 seconds
......@@ -150,6 +150,12 @@ workflow_parameters:
description: |
10x cellranger version.
- id: astrocyte
type: select
default: 'true'
regex: 'true'
description: |
10x cellranger version.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
......
......@@ -7,17 +7,36 @@
params.fastq = "$baseDir/../test_data/*.fastq.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0'
params.genomes = []
params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.genomeLocationFull = params.genomeLocation+params.genome
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = 'three'
params.chemistry = []
params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
params.version = '3.0.2'
params.astrocyte = 'false'
params.outDir = "$baseDir/output"
// Assign variables if astrocyte
if (params.astrocyte == 'false') {
params.genomes = []
params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
params.chemistry = []
params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
} else if (params.astrocyte == 'true') {
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
if (params.kitVersion == "one") {
params.chemistryParam ='SC3Pv1'
} else if (params.kitVersion == "two") {
params.chemistryParam ='SC3Pv2'
} else if (params.kitVersion == "three") {
params.chemistryParam ='SC3Pv3'
} else {
params.chemistryParam = 'auto'
}
}
params.genomeLocationFull = params.genomeLocation+params.genome
// Define regular variables
designLocation = Channel
.fromPath(params.designFile)
......@@ -84,6 +103,7 @@ chemistryParam301 = chemistryParam
chemistryParam302 = chemistryParam
process count211 {
memory '120 GB'
tag "count211-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
......@@ -115,6 +135,7 @@ process count211 {
}
process count301 {
memory '120 GB'
tag "count301-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
......@@ -147,6 +168,7 @@ process count301 {
}
process count302 {
memory '120 GB'
tag "count302-$sample"
publishDir "$outDir/${task.process}", mode: 'copy'
......
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