ncores=int(args.ncores)
# Read sample names text file
sample_names_file=args.sample_names_file
sampleNames = functions.read_sample_names(sample_names_file)
# Set input and output directories if not 'rawReads/'
in_dir=path + '/' + args.in_dir
out_dir=path + '/' +args.out_dir
out_dir_report=path + '/' + args.out_dir_report
# Create out_dir_report
functions.make_sure_path_exists(out_dir_report)
# Detect if files are gz
gz = functions.check_gz(in_dir)
# Run fastqc
Parallel(n_jobs=ncores)(delayed(qc_check)(i) for i in sampleNames)
# Number of reads per sample
os.system("Rscript bin/indexQC.R " + in_dir + " " + out_dir_report)
params_file = args.analysis_info_file
path = functions.read_parameters_file(params_file)['Working directory']
refGenome = functions.read_parameters_file(params_file)['Reference Genome']
strand = functions.read_parameters_file(params_file)['strand']
strand_piccard, strand_htseq = functions.get_strand(strand)
gtfFile = functions.read_parameters_file(params_file)['GTF File']
os.chdir(path)
# Read sample names text file
sampleNames = functions.read_sample_names()
# Set input and output directories if not '/'
in_dir = args.in_dir
out_dir = args.out_dir
functions.make_sure_path_exists(out_dir)
mapping_summary_file = args.mapping_summary_file
# Detect if files are gz
gz = functions.check_gz(in_dir)
# Count command
Parallel(n_jobs=7)(delayed(counting)(i) for i in sampleNames)
# QC
os.system("Rscript /usr/local/bin/countsLog_rnaseq.R " + out_dir + ' ' +
mapping_summary_file)
os.system("Rscript /usr/local/bin/library_proportion.R " + out_dir + ' ' +
out_dir + ' ' + gtfFile)