def run_fastqc(fastq1, fastq2, reports, tempdir, config):
"""
run fastqc on both fastq files
run trimgalore if needed, copy if not.
"""
container_ctx = helpers.get_container_ctx(config['containers'],
'fastqc',
docker_only=True)
reports_dir = os.path.join(tempdir, 'fastqc_reports')
if not os.path.exists(reports_dir):
helpers.makedirs(reports_dir)
out_html = os.path.join(reports_dir, 'fastqc_R1.html')
out_plot = os.path.join(reports_dir, 'fastqc_R1.zip')
if not os.path.getsize(fastq1) == 0:
bamutils.produce_fastqc_report(fastq1, out_html, out_plot, tempdir,
**container_ctx)
else:
warnings.warn("fastq file %s is empty, skipping fastqc" % fastq1)
out_html = os.path.join(reports_dir, 'fastqc_R2.html')
out_plot = os.path.join(reports_dir, 'fastqc_R2.zip')
if not os.path.getsize(fastq2) == 0:
bamutils.produce_fastqc_report(fastq2, out_html, out_plot, tempdir,
**container_ctx)
else:
warnings.warn("fastq file %s is empty, skipping fastqc" % fastq1)
helpers.make_tarfile(reports, reports_dir)
def run_fastqc(fastq1, fastq2, reports_dir, tempdir, containers):
"""
run fastqc on both fastq files
run trimgalore if needed, copy if not.
"""
# empty fastq files
if os.stat(fastq1).st_size < 100 and os.stat(fastq2).st_size < 100:
return
out_html = os.path.join(reports_dir, 'fastqc_R1.html')
out_plot = os.path.join(reports_dir, 'fastqc_R1.zip')
if not os.path.getsize(fastq1) == 0:
bamutils.produce_fastqc_report(fastq1,
out_html,
out_plot,
tempdir,
docker_image=containers['fastqc'])
else:
logging.getLogger("single_cell.align.tasks").warn(
"fastq file %s is empty, skipping fastqc" % fastq1)
out_html = os.path.join(reports_dir, 'fastqc_R2.html')
out_plot = os.path.join(reports_dir, 'fastqc_R2.zip')
if not os.path.getsize(fastq2) == 0:
bamutils.produce_fastqc_report(fastq2,
out_html,
out_plot,
tempdir,
docker_image=containers['fastqc'])
else:
logging.getLogger("single_cell.align.tasks").warn(
"fastq file %s is empty, skipping fastqc" % fastq1)