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()