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https://gitea.psi.ch/APOG/acsm-fairifier.git
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Added workflows folder and utils.py to support workflow generation
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184
workflows/workflow_acsm_data_PAY_2024.yaml
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184
workflows/workflow_acsm_data_PAY_2024.yaml
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name: workflow_acsm_data_PAY_2024
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steps:
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update_datachain_params:
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command: python $script_py $campaign_data_h5 $instrument_folder
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inputs:
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- script_py:
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path: pipelines/steps/update_datachain_params.py
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- campaign_data_h5:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06.h5
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- in_1:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE/2024/params/calibration_params.yaml
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implicit: true
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- in_2:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE/2024/params/limits_of_detection.yaml
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implicit: true
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- in_3:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE/2024/params/validity_thresholds.yaml
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implicit: true
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outputs:
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- out_1:
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path: pipelines/params/calibration_params.yaml
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implicit: true
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- out_2:
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path: pipelines/params/limits_of_detection.yaml
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implicit: true
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- out_3:
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path: pipelines/params/validity_thresholds.yaml
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implicit: true
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parameters:
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- instrument_folder:
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value: ACSM_TOFWARE/2024
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apply_calibration_factors:
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command: python $script_py $campaign_data_h5 $calib_yaml
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inputs:
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- script_py:
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path: pipelines/steps/apply_calibration_factors.py
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- campaign_data_h5:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06.h5
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- calib_yaml:
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path: pipelines/params/calibration_factors.yaml
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- data_descriptor_yaml:
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path: campaignDescriptor.yaml
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implicit: true
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outputs:
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- out_1:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated.csv
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implicit: true
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- out_2:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated_err.csv
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implicit: true
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- out_3:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibration_factors.csv
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implicit: true
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parameters: []
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generate_flags_diagnostics:
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command: python $script_py $data_file $flag_type
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inputs:
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- script_py:
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path: pipelines/steps/generate_flags.py
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- data_file:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06.h5
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- validity_thresholds_yaml:
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path: pipelines/params/validity_thresholds.yaml
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implicit: true
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outputs:
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- flags_csv:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_meta_flags.csv
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implicit: true
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parameters:
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- flag_type:
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value: diagnostics
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generate_flags_species:
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command: python $script_py $data_file $flag_type
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inputs:
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- script_py:
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path: pipelines/steps/generate_flags.py
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- data_file:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06.h5
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- calibration_params_yaml:
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path: pipelines/params/calibration_params.yaml
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implicit: true
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- flag_in_0:
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description: automated or cpc flag
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_meta_flags.csv
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implicit: true
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outputs:
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- flags_csv:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_timeseries_flags.csv
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implicit: true
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parameters:
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- flag_type:
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value: species
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prepare_ebas_submission:
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command: python $script_py $in_1 $in_2 $in_3 $in_4 $month_range
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inputs:
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- script_py:
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path: pipelines/steps/prepare_ebas_submission.py
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- in_1:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated.csv
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- in_2:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated_err.csv
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- in_3:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibration_factors.csv
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- in_4:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_timeseries_flags.csv
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- lod:
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path: pipelines/params/"limits_of_detection.yaml
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implicit: true
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- station:
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path: pipelines/params/"station_params.yaml
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implicit: true
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outputs:
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- out_1:
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path: data/PAY_ACSM-092_2024.txt
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implicit: true
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- out_2:
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path: data/PAY_ACSM-092_FLAGS_2024.txt
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implicit: true
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parameters:
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- month_range:
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value: 2-3
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visualize_diagnostic_variables:
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command: python $script_py $data_file $dataset_name $flags_dataset_name $x_var
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$y_vars $fig_0_VaporizerTemp_C $fig_1_FlowRate_ccs $fig_2_FilamentEmission_mA
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$fig_3_ABsamp
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inputs:
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- script_py:
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path: pipelines/steps/visualize_datatable_vars.py
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- data_file:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06.h5
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- alternative_flags_csv:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_meta_flags.csv
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implicit: true
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outputs:
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- fig_0_VaporizerTemp_C:
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path: figures/fig_0_VaporizerTemp_C.html
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- fig_1_FlowRate_ccs:
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path: figures/fig_1_FlowRate_ccs.html
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- fig_2_FilamentEmission_mA:
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path: figures/fig_2_FilamentEmission_mA.html
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- fig_3_ABsamp:
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path: figures/fig_3_ABsamp.html
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parameters:
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- dataset_name:
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value: ACSM_TOFWARE/2024/ACSM_PAY_2024_meta.txt/data_table
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- flags_dataset_name:
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value: ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_meta.txt/data_table
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- x_var:
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value: t_base
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- y_vars:
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value:
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- VaporizerTemp_C
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- FlowRate_ccs
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- FilamentEmission_mA
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- ABsamp
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workflow_acsm_data_PAY_2024_step:
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command: python $script_py $in_1 $in_2 $in_3 $in_4 $month_range
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inputs:
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- script_py:
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path: pipelines/steps/prepare_ebas_submission.py
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- in_1:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated.csv
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- in_2:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibrated_err.csv
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- in_3:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_processed/2024/ACSM_PAY_2024_timeseries_calibration_factors.csv
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- in_4:
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path: data/collection_PAY_2024_2025-06-06_2025-06-06/ACSM_TOFWARE_flags/2024/ACSM_PAY_2024_timeseries_flags.csv
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- lod:
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path: pipelines/params/"limits_of_detection.yaml
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implicit: true
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- station:
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path: pipelines/params/"station_params.yaml
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implicit: true
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outputs:
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- out_1:
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path: data/PAY_ACSM-092_2024.txt
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implicit: true
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- out_2:
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path: data/PAY_ACSM-092_FLAGS_2024.txt
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implicit: true
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parameters:
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- month_range:
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value: 2-3
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