diff --git a/opencga-app/app/analysis/qc/family_qc/family_qc.py b/opencga-app/app/analysis/qc/family_qc/family_qc.py index 59ceaef3a2..88d3413816 100644 --- a/opencga-app/app/analysis/qc/family_qc/family_qc.py +++ b/opencga-app/app/analysis/qc/family_qc/family_qc.py @@ -12,7 +12,7 @@ LOGGER = logging.getLogger('variant_qc_logger') class FamilyQCExecutor: - def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job_id, sample_ids, id_): + def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, sample_ids, id_): """Create output dir :param str vcf_file: VCF input file path @@ -21,7 +21,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job :param str config: Configuration file path :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1) :param list sample_ids: Sample IDs from the VCF file - :param str job_id: ID from the executed job :param str id_: ID from the info JSON file """ self.vcf_file = vcf_file @@ -29,7 +28,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job self.bam_file = bam_file self.config = config self.output_parent_dir = output_parent_dir - self.job_id = job_id self.sample_ids = sample_ids self.id_ = id_ diff --git a/opencga-app/app/analysis/qc/individual_qc/individual_qc.py b/opencga-app/app/analysis/qc/individual_qc/individual_qc.py index 37d51360e9..075087ff98 100644 --- a/opencga-app/app/analysis/qc/individual_qc/individual_qc.py +++ b/opencga-app/app/analysis/qc/individual_qc/individual_qc.py @@ -11,7 +11,7 @@ LOGGER = logging.getLogger('variant_qc_logger') class IndividualQCExecutor: - def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job_id, sample_ids, id_): + def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, sample_ids, id_): """Create output dir :param str vcf_file: VCF input file path @@ -20,7 +20,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job :param str config: Configuration file path :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1) :param list sample_ids: Sample IDs from the VCF file - :param str job_id: ID from the executed job :param str id_: ID from the info JSON file """ self.vcf_file = vcf_file @@ -28,7 +27,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job self.bam_file = bam_file self.config = config self.output_parent_dir = output_parent_dir - self.job_id = job_id self.sample_ids = sample_ids self.id_ = id_ diff --git a/opencga-app/app/analysis/qc/sample_qc/sample_qc.py b/opencga-app/app/analysis/qc/sample_qc/sample_qc.py index 021f0d76a0..463651c32d 100644 --- a/opencga-app/app/analysis/qc/sample_qc/sample_qc.py +++ b/opencga-app/app/analysis/qc/sample_qc/sample_qc.py @@ -19,7 +19,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job :param str config: Configuration file path :param str output_parent_dir: Output directory path for the id_ (e.g. /path/to/outdir/id1) :param list sample_ids: Sample IDs from the VCF file - :param str job_id: ID from the executed job :param str id_: ID from the info JSON file """ self.vcf_file = vcf_file @@ -27,7 +26,6 @@ def __init__(self, vcf_file, info_file, bam_file, config, output_parent_dir, job self.bam_file = bam_file self.config = config self.output_parent_dir = output_parent_dir - self.job_id = job_id self.sample_ids = sample_ids self.id_ = id_ @@ -81,9 +79,8 @@ def bcftools_stats(self, vcf_file): bam_file = "" config = "" output_parent_dir = "/tmp/qc_tests/" - job_id = "" sample_ids = [] id_ = "" se = SampleQCExecutor(vcf_file=vcf_file, info_file=info_file, bam_file=bam_file, config=config, - output_parent_dir=output_parent_dir, job_id=job_id, sample_ids=sample_ids, id_=id_) + output_parent_dir=output_parent_dir, sample_ids=sample_ids, id_=id_) sys.exit(se.run()) diff --git a/opencga-app/app/analysis/qc/variant_qc.main.py b/opencga-app/app/analysis/qc/variant_qc.main.py index 98688da17b..263686e869 100644 --- a/opencga-app/app/analysis/qc/variant_qc.main.py +++ b/opencga-app/app/analysis/qc/variant_qc.main.py @@ -39,8 +39,6 @@ def get_parser(): help='configuration file path') parser.add_argument('-o', '--output-dir', dest='output_dir', help='output directory path') - parser.add_argument('--job-id', dest='job_id', - help='job ID') parser.add_argument('-l', '--log-level', dest='log_level', default='INFO', choices=['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'], @@ -196,7 +194,6 @@ def main(): qc_type = args.qc_type config = args.config output_dir = os.path.realpath(os.path.expanduser(args.output_dir)) - job_id = args.job_id # Setting up logger logger = create_logger(args.log_level, output_dir) @@ -228,7 +225,6 @@ def main(): bam_file=bam_files[i], config=config, output_parent_dir=qc_outdir_fpath, - job_id=job_id, sample_ids=sample_ids, id_=id_ ).run()