-
Notifications
You must be signed in to change notification settings - Fork 0
/
visium_readzs.config
36 lines (29 loc) · 1.44 KB
/
visium_readzs.config
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
/*
========================================================================================
Nextflow config file for running minimal tests
========================================================================================
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run salzmanlab/readzs -profile small_test_data
----------------------------------------------------------------------------------------
*/
params {
input = "/oak/stanford/groups/horence/JuliaO/nf-readzs/visium/${params.runName}/samplesheet_readzs.csv"
useChannels = false
chr_lengths = "/oak/stanford/groups/horence/kaitlin/ref_files/mm10_chrLength.txt"
libType = "10X"
isSICILIAN = false
isCellranger = true
metadata = "/oak/stanford/groups/horence/JuliaO/visium_analysis/notebooks/output/visium_meta/meta_${params.runName}.tsv"
minCellsPerWindowOnt = 10
minCtsPerCell = 5
ontologyCols = "pixquant"
annotation_bed = "/oak/stanford/groups/horence/kaitlin/annotation_beds/cleaned_mm10_genes.bed"
gff = "/oak/stanford/groups/horence/kaitlin/ref_files/gencode.vM26.annotation.gff3"
}
params.outdir = "/oak/stanford/groups/horence/JuliaO/nf-readzs/visium/${params.runName}"
workDir = "/scratch/groups/horence/JuliaO/nf-readzs/work"
params.tracedir = "/oak/stanford/groups/horence/JuliaO/nf-readzs/visium/${params.runName}/pipeline_info"
tower {
enabled = true
}