diff --git a/metatlas/untargeted/run_untargeted_pipeline.py b/metatlas/untargeted/run_untargeted_pipeline.py index 9ec90d88..77232b30 100644 --- a/metatlas/untargeted/run_untargeted_pipeline.py +++ b/metatlas/untargeted/run_untargeted_pipeline.py @@ -36,16 +36,15 @@ def main(): ##### Submitting new MZmine jobs that are "initialized" mzm.submit_mzmine_jobs_to_gnps2(new_projects=new_projects,direct_input=args.direct_input,skip_mzmine_submit=step_bools['mzmine_submit'], \ - overwrite_mzmine=args.overwrite_mzmine) + overwrite_mzmine=args.overwrite_mzmine, output_dir=args.output_dir, skip_mirror_raw_data=args.skip_mirror_raw_data, + raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir) ##### Checking and updating status of FBMN jobs in LIMS mzm.update_fbmn_status_from_gnps2(direct_input=args.direct_input,skip_fbmn_status=step_bools['fbmn_status']) ##### Submitting new FBMN jobs to GNPS2 mzm.submit_fbmn_jobs_to_gnps2(output_dir=args.output_dir, overwrite_fbmn=args.overwrite_fbmn, overwrite_buddy=args.overwrite_buddy, direct_input=args.direct_input, \ - skip_fbmn_submit=step_bools['fbmn_submit'], skip_buddy_submit=step_bools['buddy_submit'], \ - skip_mirror_raw_data=args.skip_mirror_raw_data, skip_mirror_mzmine_results=args.skip_mirror_mzmine_results, \ - raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir) + skip_fbmn_submit=step_bools['fbmn_submit']) ##### Submitting new BUDDY jobs to GNPS2 mzm.submit_buddy_jobs_to_gnps2(output_dir=args.output_dzir, overwrite_buddy=args.overwrite_buddy, direct_input=args.direct_input, \ diff --git a/metatlas/untargeted/tools.py b/metatlas/untargeted/tools.py index 5c839338..10391c95 100644 --- a/metatlas/untargeted/tools.py +++ b/metatlas/untargeted/tools.py @@ -163,9 +163,9 @@ def zip_and_upload_untargeted_results( Min_features_admissible is 0 (default) if you want the function to zip and upload only when there are more than 0 features """ if skip_zip_upload: - logging.info("Skipping Step 7/7: Zipping up and (optionally) uploading output folders to gdrive...") + logging.info("Skipping zipping up and (optionally) uploading output folders to gdrive...") return - logging.info("Step 7/7: Zipping up and (optionally) uploading output folders to gdrive...") + logging.info("Zipping up and (optionally) uploading output folders to gdrive...") df = get_table_from_lims('untargeted_tasks') df = filter_common_bad_project_names(df) if direct_input is not None: @@ -1300,9 +1300,9 @@ def update_fbmn_status_from_gnps2( to a csv list of project names if you only want to run this function on specific untargeted_tasks """ if skip_fbmn_status: - logging.info('Skipping Step 4/7: Checking and updating status of FBMN jobs in LIMS...') + logging.info('Skipping checking and updating status of FBMN jobs in LIMS...') return - logging.info('Step 4/7: Checking and updating status of FBMN jobs in LIMS...') + logging.info('Checking and updating status of FBMN jobs in LIMS...') tasktype='fbmn' df = get_table_from_lims('untargeted_tasks') df = filter_common_bad_project_names(df) @@ -1536,9 +1536,9 @@ def update_new_untargeted_tasks( space and labkey doesn't allow this """ if skip_sync: - logging.info('Skipping Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...') + logging.info('Skipping syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...') return - logging.info('Step 1/7: Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...') + logging.info('Syncing LIMS and NERSC to identify new projects with raw data that are not yet in the untargeted task list...') # Get lcmsrun table and subset df = get_table_from_lims('lcmsrun_plus') df = df[pd.notna(df['mzml_file'])] @@ -1606,9 +1606,8 @@ def update_new_untargeted_tasks( lims_untargeted_table_updater['conforming_filenames'] = True lims_untargeted_table_updater['file_conversion_complete'] = True lims_untargeted_table_updater['output_dir'] = output_dir - if validate_names is True: - _, validate_machine_name, _ = vfn.field_exists(PurePath(project_name), field_num=6) - if validate_names is False: + _, validate_machine_name, _ = vfn.field_exists(PurePath(project_name), field_num=6) + if validate_machine_name is None: validate_machine_name = "EXP120A" # Assume stricter parameters for unvalidated machine name logging.info(tab_print("Notice! Using stricter mzmine parameters because machine name cannot be inferred from project name.", 2)) if validate_machine_name.lower() in ("iqx", "idx"): @@ -1617,6 +1616,7 @@ def update_new_untargeted_tasks( else: mzmine_running_parameters = "Default" mzmine_parameter = 2 + logging.info(tab_print("Using mzmine parameters for %s: "%(mzmine_running_parameters), 2)) lims_untargeted_table_updater['mzmine_parameter_sheet'] = mzmine_running_parameters lims_untargeted_table_updater['mzmine_parameter_row'] = mzmine_parameter @@ -1690,9 +1690,9 @@ def submit_mzmine_jobs_to_gnps2( to a csv list of project names if you only want to run this function on specific untargeted_tasks """ if skip_mzmine_submit: - logging.info('Skipping Step 3/7: Submitting new MZmine jobs...') + logging.info('Skipping submitting new MZmine jobs...') return - logging.info('Step 3/7: Submitting new MZmine jobs...') + logging.info('Submitting new MZmine jobs...') tasktype = 'mzmine' df = get_table_from_lims('untargeted_tasks') df = filter_common_bad_project_names(df) @@ -1806,9 +1806,9 @@ def update_mzmine_status_from_gnps2( to a csv list of project names if you only want to run this function on specific untargeted_tasks """ if skip_mzmine_status: - logging.info('Skipping Step 3/7: Checking and updating status of MZMine jobs in LIMS...') + logging.info('Skipping checking and updating status of MZMine jobs in LIMS...') return - logging.info('Step 3/7: Checking and updating status of MZMine jobs in LIMS...') + logging.info('Checking and updating status of MZMine jobs in LIMS...') tasktype='mzmine' df = get_table_from_lims('untargeted_tasks') df = filter_common_bad_project_names(df) @@ -2053,9 +2053,9 @@ def download_fbmn_results_from_gnps2( to a csv list of project names if you only want to run this function on specific untargeted_tasks """ if skip_fbmn_download: - logging.info('Skipping Step 6/7: Checking for completed FBMN jobs and downloading results...') + logging.info('Skipping checking for completed FBMN jobs and downloading results...') return - logging.info('Step 6/7: Checking for completed FBMN jobs and downloading results...') + logging.info('Checking for completed FBMN jobs and downloading results...') tasktype='fbmn' df = get_table_from_lims('untargeted_tasks') df = filter_common_bad_project_names(df)