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Allow GNPS2 mirror to be parameterized and passed as command line argument #952

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merged 2 commits into from
Oct 10, 2024
Merged

Allow GNPS2 mirror to be parameterized and passed as command line argument #952

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12704c6
Allow GNPS2 mirror to be parameterized and passed as command line arg…
bkieft-usa Oct 10, 2024
927317c
Merge branch 'main' into untargeted_dev
bkieft-usa Oct 10, 2024
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5 changes: 4 additions & 1 deletion metatlas/untargeted/run_untargeted_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def main():

##### Step 5/7: Submitting new FBMN jobs to GNPS2
mzm.submit_fbmn_jobs(output_dir=args.output_dir, overwrite_fbmn=args.overwrite_fbmn, direct_input=args.direct_input, skip_fbmn_submit=step_bools[4], \
raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir)
mirror_raw_data=args.mirror_raw_data, mirror_mzmine_results=args.mirror_mzmine_results, raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir)

##### Step 6/7: Checking for completed FBMN jobs and downloading results
mzm.download_fbmn_results(output_dir=args.output_dir, overwrite_fbmn=args.overwrite_fbmn,direct_input=args.direct_input, \
Expand Down Expand Up @@ -82,6 +82,9 @@ def add_arguments(parser):
parser.add_argument('--nonpolar_solvent_front', type=float, default=0.5, help='Retention time to use as C18/LIPID solvent front (mins) for filtering features')
## Step 3 only
parser.add_argument('--overwrite_mzmine', type=bool, default=False, help='Overwrite existing mzmine results files that are already in the output directory')
## Step 5 only
parser.add_argument('--mirror_raw_data', type=bool, default=True, help='Mirror raw data files to GNPS2')
parser.add_argument('--mirror_mzmine_results', type=bool, default=True, help='Mirror mzmine results files to GNPS2')
## Step 7 only
parser.add_argument('--download_dir', type=str, default='/global/cfs/cdirs/metatlas/projects/untargeted_outputs', help='Path to the download folder')
parser.add_argument('--overwrite_zip',type=bool, default=False, help='Overwrite existing zip files in download folder')
Expand Down
11 changes: 7 additions & 4 deletions metatlas/untargeted/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1153,6 +1153,8 @@ def submit_fbmn_jobs(
overwrite_fbmn: bool,
output_dir: str,
skip_fbmn_submit: bool,
mirror_raw_data: bool,
mirror_mzmine_results: bool,
direct_input: Optional[str] = None,
raw_data_dir: Optional[str] = None,
raw_data_subdir: Optional[str] = None
Expand Down Expand Up @@ -1228,8 +1230,10 @@ def submit_fbmn_jobs(

# Get mzmine results files and raw data to GNPS2 before starting FBMN job
logging.info(tab_print("Ensuring MZmine results are at GNPS2 before submitting FBMN job...", 2))
mirror_mzmine_results_to_gnps2(project=project_name,polarity=polarity,output_dir=output_dir,username="bpbowen")
mirror_raw_data_to_gnps2(project=project_name,polarity=polarity,username="bpbowen",raw_data_dir=raw_data_dir,raw_data_subdir=raw_data_subdir)
if mirror_mzmine_results is True:
mirror_mzmine_results_to_gnps2(project=project_name,polarity=polarity,output_dir=output_dir,username="bpbowen")
if mirror_raw_data is True:
mirror_raw_data_to_gnps2(project=project_name,polarity=polarity,username="bpbowen",raw_data_dir=raw_data_dir,raw_data_subdir=raw_data_subdir)

description = '%s_%s'%(project_name,polarity)
spectra_file = f'USERUPLOAD/bpbowen/untargeted_tasks/{project_name}_{polarity}/{project_name}_{polarity}.mgf'
Expand Down Expand Up @@ -1874,8 +1878,7 @@ def update_new_untargeted_tasks(
output_dir: str,
direct_input: Optional[str] = None,
raw_data_dir: Optional[str] = None,
raw_data_subdir: Optional[str] = None,

raw_data_subdir: Optional[str] = None
) -> None:
"""
This script is called by run_mzmine.py before the untargeted pipeline kicks off
Expand Down
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