script/debug-bwa.R

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

# p2578
setwd("/scratch/gtan/debug/quickDebug")
library(ezRun)
param = list()
param[['cores']] = '8'
param[['ram']] = '16'
param[['scratch']] = '100'
param[['node']] = ''
param[['process_mode']] = 'SAMPLE'
param[['samples']] = 'C8102P,C5401P,C6701P,C8902-7P,C8301P'
param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26'
param[['paired']] = 'true'
param[['algorithm']] = 'mem'
param[['cmdOptions']] = ''
param[['trimAdapter']] = 'false'
param[['trimLeft']] = '0'
param[['trimRight']] = '0'
param[['minTailQuality']] = '0'
param[['minAvgQuality']] = '0'
param[['minReadLength']] = '20'
param[['specialOptions']] = ''
param[['mail']] = 'ge.tan@fgcz.ethz.ch'
param[['dataRoot']] = '/srv/gstore/projects'
param[['resultDir']] = 'p2578/BWA_26020_2018-11-10--19-40-49'
output = list()
output[['Name']] = 'C8902-7P'
output[['BAM [File]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P.bam'
output[['BAI [File]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P.bam.bai'
output[['IGV Starter [Link]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P-igv.jnlp'
output[['Species']] = 'Homo sapiens (human)'
output[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26'
output[['paired']] = 'true'
output[['refFeatureFile']] = ''
output[['strandMode']] = ''
output[['Read Count']] = '27955406'
output[['IGV Starter [File]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P-igv.jnlp'
output[['IGV Session [File]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P-igv.xml'
output[['PreprocessingLog [File]']] = 'p2578/BWA_26020_2018-11-10--19-40-49/C8902-7P_preprocessing.log'
output[['Condition [Factor]']] = ''
output[['Sample Id [B-Fabric]']] = 'bfs_164963'
output[['FragmentSize [Characteristic]']] = '0'
output[['SampleConc [Characteristic]']] = '85'
output[['Tube [Characteristic]']] = 'p2578_3757/16'
output[['Index [Characteristic]']] = 'TCCTGAGC'
output[['PlatePosition [Characteristic]']] = 'usermade_caf_'
output[['LibConc_100_800bp [Characteristic]']] = '0'
output[['LibConc_qPCR [Characteristic]']] = '0'
output[['InputAmount [Characteristic]']] = '0'
input = list()
input[['Name']] = 'C8902-7P'
input[['Condition']] = ''
input[['Read1']] = 'p2578/HiSeq2500_20171103_RUN396_o3757/20171103.B-C8902-7P_R1.fastq.gz'
input[['Read2']] = 'p2578/HiSeq2500_20171103_RUN396_o3757/20171103.B-C8902-7P_R2.fastq.gz'
input[['Species']] = 'Homo sapiens (human)'
input[['FragmentSize']] = '0'
input[['SampleConc']] = '85'
input[['Tube']] = 'p2578_3757/16'
input[['Index']] = 'TCCTGAGC'
input[['PlatePosition']] = 'usermade_caf_'
input[['LibConc_100_800bp']] = '0'
input[['LibConc_qPCR']] = '0'
input[['Adapter1']] = 'NA'
input[['Adapter2']] = 'NA'
input[['strandMode']] = 'NA'
input[['LibraryPrepKit']] = 'ATAC '
input[['EnrichmentMethod']] = 'None'
input[['InputAmount']] = '0'
input[['Read Count']] = '27955406'
input[['Sample Id']] = 'bfs_164963'
EzAppBWA$new()$run(input=input, output=output, param=param)