def runFastqc(infiles, outfile): '''run Fastqc on each input file. convert sra files to fastq and check mapping qualities are in solexa format. Perform quality control checks on reads from .fastq files. ''' # MM: only pass the contaminants file list if requested by user, # do not make this the default behaviour if PARAMS['use_custom_contaiminants']: m = PipelineMapping.FastQc(nogroup=PARAMS["readqc_no_group"], outdir=PARAMS["exportdir"] + "/fastqc", contaminants=PARAMS['contaminants_path'], qual_format=PARAMS['qual_format']) else: m = PipelineMapping.FastQc(nogroup=PARAMS["readqc_no_group"], outdir=PARAMS["exportdir"] + "/fastqc", qual_format=PARAMS['qual_format']) if PARAMS["general_reconcile"] == 1: infiles = infiles.replace("processed.dir/trimmed", "reconciled.dir/trimmed") statement = m.build((infiles,), outfile) job_memory = "8G" P.run()
def runFastqc(infiles, outfile): '''convert sra files to fastq and check mapping qualities are in solexa format. Perform quality control checks on reads from .fastq files.''' to_cluster = True m = PipelineMapping.FastQc(nogroup=PARAMS["readqc_no_group"]) statement = m.build((infiles, ), outfile) P.run()
def qcDemuxedReads(infile, outfile): ''' Run fastqc on the post demuxing and trimmed reads''' m = PipelineMapping.FastQc(nogroup=False, outdir="fastqc") statement = m.build((infile, ), outfile) exportdir = "fastqc" P.run()