def flash2(cls, args):
"""executes the fastqc binary on fq_fp."""
try:
result = cls._flash2(args, _err_to_out=True)
except sh.ErrorReturnCode as err:
raise pipeline_error.shError(err.stdout, err.stderr)
if result.exit_code != 0:
raise pipeline_error.shError(result.stdout, result.stderr)
return result
def se_trim(cls, args):
"""executes the trimmomatic binary."""
try:
result = cls._se_trim(args, _err_to_out=True)
except sh.ErrorReturnCode as err:
raise pipeline_error.shError(err.stdout, err.stderr)
if result.exit_code != 0:
raise pipeline_error.shError(result.stdout, result.stderr)
return result
def multiqc(cls, inputs_d, out_dir, job_desc):
"""executes multiqc on its inputs directory."""
try:
if (job_desc and job_desc.strip()):
result = cls._multiqc('--title', job_desc.strip(), '-o', out_dir, inputs_d)
else:
result = cls._multiqc('-o', out_dir, inputs_d)
except sh.ErrorReturnCode as err:
raise pipeline_error.shError(err.stdout, err.stderr)
if result.exit_code != 0:
raise pipeline_error.shError(result.stdout, result.stderr)
return result
def fastqc(cls, fq_fp, out_fp):
"""executes the fastqc binary on fq_fp.
Args:
fq_fp: path to fastq file
out_fp: output directory outputs/multiqc_input
Raises:
`nephele2.pipelines.pipeline_error.shError`
"""
try:
result = cls._fastqc('-o', out_fp, fq_fp)
except sh.ErrorReturnCode as err:
raise pipeline_error.shError(err.stdout, err.stderr)
if result.exit_code != 0:
raise pipeline_error.shError(result.stdout, result.stderr)
return result