script/debug-CellRangerATAC.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

setwd("/scratch/gtan/dev/quickdev")
library(ezRun)
param = list()
param[['cores']] = '12'
param[['ram']] = '40'
param[['scratch']] = '200'
param[['node']] = ''
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'Control_WT_-_Mac,SPTA_-_Mac'
param[['name']] = 'CellRangerATACCount'
param[['refBuild']] = 'Mus_musculus/GENCODE/GRCm38.p6/Annotation/Release_M23-2019-11-05'
param[['refFeatureFile']] = 'genes.gtf'
param[['featureLevel']] = 'gene'
param[['cmdOptions']] = ''
param[['specialOptions']] = ''
param[['mail']] = 'ge.tan@fgcz.ethz.ch'
param[['dataRoot']] = '/srv/gstore/projects'
param[['resultDir']] = 'p3162/CellRangerCountATAC_38277_2019-07-22--23-54-13'
output = list()
output[['Name']] = 'Control_WT_-_Mac'
output[['Species']] = 'Mus musculus (house mouse)'
output[['refBuild']] = 'Mus_musculus/GENCODE/GRCm38.p6/Annotation/Release_M23-2019-11-05'
output[['refFeatureFile']] = 'genes.gtf'
output[['featureLevel']] = 'gene'
output[['ResultDir [File]']] = 'p3162/CellRangerCountATAC_38277_2019-07-22--23-54-13/Control_WT_-_Mac'
output[['Report [Link]']] = 'p3162/CellRangerCountATAC_38277_2019-07-22--23-54-13/Control_WT_-_Mac/web_summary.html'
output[['CountMatrix [Link]']] = 'p3162/CellRangerCountATAC_38277_2019-07-22--23-54-13/Control_WT_-_Mac/filtered_peak_bc_matrix'
output[['Sample Id [B-Fabric]']] = 'bfs_200130'
output[['Order Id [B-Fabric]']] = '5835'
input = list()
input[['Name']] = 'Control_WT_-_Mac'
input[['Condition']] = ''
input[['Species']] = 'Mus musculus (house mouse)'
input[['FragmentSize']] = '0'
input[['SampleConc']] = '1'
input[['Tube']] = 'p3162_5835/2'
input[['Sample Id']] = 'bfs_200130'
input[['PlatePosition']] = '1_B1'
input[['LibConc_100_800bp']] = '0'
input[['LibConc_qPCR']] = '0'
input[['RIN']] = '0'
input[['Adapter1']] = 'NA'
input[['Adapter2']] = 'NA'
input[['strandMode']] = 'NA'
input[['LibraryPrepKit']] = '10X Genomics Single Cell, V3'
input[['EnrichmentMethod']] = 'None'
input[['InputAmount']] = 'NA'
input[['Order Id']] = '5835'
input[['PlateName']] = 'DSC 20_10X'
input[['RawDataDir']] = 'p3162/NextSeq500_20200228_NS385_o6773/Control_WT_-_Mac.tar'
input[['Read1']] = 'p3162/NextSeq500_20200228_NS385_o6773/Control_WT_-_Mac/Control_WT_-_Mac_S1_L001_R2_001.fastq.gz'
input[['Read Count']] = '129165820'
debug(ezMethodCellRangerATAC)
EzAppCellRangerATAC$new()$run(input=input, output=output, param=param)