Commit 51ff8a09 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Fix configs and refs

parent abd059b2
Pipeline #7565 passed with stages
in 9 minutes and 27 seconds
......@@ -12,27 +12,27 @@ process {
cpus = 1
memory = '1 GB'
withLabel: checkDesignFile {
withName: checkDesignFile {
cpus = 2
memory = '1 GB'
}
withLabel: count211 {
withName: count211 {
cpus = 2
memory = '30 GB'
}
withLabel: count302 {
withName: count302 {
cpus = 2
memory = '30 GB'
}
withLabel: count310 {
withName: count310 {
cpus = 2
memory = '30 GB'
}
withLabel: versions {
withName: versions {
cpus = 3
memory = '1 GB'
}
withLabel: multiqc {
withName: multiqc {
cpus = 1
memory = '1 GB'
}
......
......@@ -9,25 +9,25 @@ process {
withLabel: checkDesignFile {
executor = 'local'
}
withLabel: count211 {
withName: count211 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count220 {
withName: count220 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count302 {
withName: count302 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count310 {
withName: count310 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: count400 {
withName: count400 {
queue = '128GB,256GB,256GBv1,384GB'
}
withLabel: versions {
withName: versions {
executor = 'local'
}
withLabel: multiqc {
withName: multiqc {
executor = 'local'
}
}
......@@ -22,7 +22,6 @@ params.name = "run"
params.fastq = "test_data/mu.v3s1r500/*.fastq.gz"
params.designFile = "test_data/mu.v3s1r500/design.csv"
params.genome = 'mm10-2020-A'
params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = '3GEXv3'
......@@ -39,7 +38,11 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
// Define variables if astrocyte (or from config)
if (params.astrocyte) {
print("Running under astrocyte")
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
if (params.version == "4.0.0") {
params.genomeLocation = '/project/apps_database/cellranger/refdata-gex-'
} else {
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
}
if (params.kitVersion == "3GEXv1") {
params.chemistryParam ='SC3Pv1'
} else if (params.kitVersion == "3GEXv2") {
......
profiles {
standard {
includeConfig 'configs/biohpc.config'
includeConfig 'configs/cluster.config'
}
biohpc {
includeConfig 'configs/biohpc.config'
......
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