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kalenkovich / reproducible-MEEG

Code that attempts to reproduce "A Reproducible MEG/EEG Group Study With the MNE Software" by Jas et al., 2018
MIT License
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clean the paths #8

Open kalenkovich opened 3 years ago

kalenkovich commented 3 years ago

There are two places where paths make it hard to understand what is going on:

  1. Templates in Snakefile:

    ```python
# Templates
run_template = (openneuro_maxfiltered_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                'sub-{subject_number}_ses-meg_task-facerecognition_run-{run_id}_proc-sss_meg.fif')
events_template = (bids_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                'sub-{subject_number}_ses-meg_task-facerecognition_run-{run_id}_events.tsv')
filtered_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                     'sub-{subject_number}_ses-meg_task-facerecognition_run-{run_id}_filteredHighPass{l_freq}.fif')
ica_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                'sub-{subject_number}_ses-meg_task-facerecognition_filtered.fif')
maxfilter_log_template = (openneuro_maxfiltered_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                          'sub-{subject_number}_ses-meg_task-facerecognition_run-{run_id}_proc-sss_log.txt')
bad_channels_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                         'sub-{subject_number}_ses-meg_task-facerecognition_run-{run_id}_bads.fif')
concatenated_raw_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                             'sub-{subject_number}_ses-meg_task-facerecognition_proc-sss_megConcatenated.fif')
concatenated_events_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                                'sub-{subject_number}_ses-meg_task-facerecognition_proc-sss_eventsConcatenated.fif')
epoched_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                         'sub-{subject_number}_ses-meg_task-facerecognition_epo.fif')
ecg_epochs_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                       'sub-{subject_number}_ses-meg_task-facerecognition_ecgEpochs.fif')
eog_epochs_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                       'sub-{subject_number}_ses-meg_task-facerecognition_eogEpochs.fif')
artifact_components_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                       'sub-{subject_number}_ses-meg_task-facerecognition_artifactComponents.npz')
epochs_cleaned_template = (preprocessing_dir / 'sub-{subject_number}' / 'ses-meg' / 'meg' /
                           'sub-{subject_number}_ses-meg_task-facerecognition_epoCleaned.fif')
```

  2. Snakemake output

    A piece of a sample output ```sh [Tue Jul 27 14:34:32 2021] rule clean_epochs: input: E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_filtered.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\0 1_reproduction\data\bids\derivatives\01_preprocessing\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_artifactComponents.npz, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocess ing\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_epo.fif output: E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_epoCleaned.fif jobid: 672 wildcards: subject_number=16 [Tue Jul 27 14:34:32 2021] localrule all: input: E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids \sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgeni i_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-01\ses-meg\meg\ sub-01_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reprod ucing-reproducible\01_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task- facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\0 1_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task-facerecognition_run- 05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-02\ses-meg\meg\sub-02_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\ bids\sub-03\ses-meg\meg\sub-03_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-03\ses-meg\meg\sub-03_ses-meg_task-facerecognition_run-02_events.tsv, E:\Ev genii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-03\ses-meg\meg\sub-03_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-03\ses-meg\ meg\sub-03_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-03\ses-meg\meg\sub-03_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\re producing-reproducible\01_reproduction\data\bids\sub-03\ses-meg\meg\sub-03_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-04\ses-meg\meg\sub-04_ses-meg_t ask-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-04\ses-meg\meg\sub-04_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducib le\01_reproduction\data\bids\sub-04\ses-meg\meg\sub-04_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-04\ses-meg\meg\sub-04_ses-meg_task-facerecognition_ run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-04\ses-meg\meg\sub-04_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\d ata\bids\sub-04\ses-meg\meg\sub-04_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses-meg\meg\sub-05_ses-meg_task-facerecognition_run-01_events.tsv, E :\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses-meg\meg\sub-05_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses- meg\meg\sub-05_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses-meg\meg\sub-05_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovic h\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses-meg\meg\sub-05_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-05\ses-meg\meg\sub-05_ses-m eg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reprod ucible\01_reproduction\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognit ion_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproducti on\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_run-06_events.ts v, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ses-meg\meg\sub-07_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ ses-meg\meg\sub-07_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ses-meg\meg\sub-07_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenk ovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ses-meg\meg\sub-07_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ses-meg\meg\sub-07_s es-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-07\ses-meg\meg\sub-07_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-re producible\01_reproduction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facereco gnition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reprod uction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facerecognition_run-05_event s.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-08\ses-meg\meg\sub-08_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub -09\ses-meg\meg\sub-09_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-09\ses-meg\meg\sub-09_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Ka lenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-09\ses-meg\meg\sub-09_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-09\ses-meg\meg\sub- 09_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-09\ses-meg\meg\sub-09_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducin g-reproducible\01_reproduction\data\bids\sub-09\ses-meg\meg\sub-09_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-10\ses-meg\meg\sub-10_ses-meg_task-face recognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-10\ses-meg\meg\sub-10_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_re production\data\bids\sub-10\ses-meg\meg\sub-10_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-10\ses-meg\meg\sub-10_ses-meg_task-facerecognition_run-04_e vents.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-10\ses-meg\meg\sub-10_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids \sub-10\ses-meg\meg\sub-10_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\sub-11_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgeni i_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\sub-11_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\ sub-11_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\sub-11_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reprod ucing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\sub-11_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-11\ses-meg\meg\sub-11_ses-meg_task- facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\0 1_reproduction\data\bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run- 03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\ bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_run-06_events.tsv, E:\Ev genii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\meg\sub-13_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\ meg\sub-13_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\meg\sub-13_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\re producing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\meg\sub-13_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\meg\sub-13_ses-meg_t ask-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-13\ses-meg\meg\sub-13_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducib le\01_reproduction\data\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_ run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\d ata\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_run-05_events.tsv, E :\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-15\ses- meg\meg\sub-15_ses-meg_task-facerecognition_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-15\ses-meg\meg\sub-15_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovic h\reproducing-reproducible\01_reproduction\data\bids\sub-15\ses-meg\meg\sub-15_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-15\ses-meg\meg\sub-15_ses-m eg_task-facerecognition_run-04_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-15\ses-meg\meg\sub-15_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reprod ucible\01_reproduction\data\bids\sub-15\ses-meg\meg\sub-15_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognit ion_run-01_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_run-02_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproducti on\data\bids\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_run-03_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_run-04_events.ts v, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_run-05_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\sub-16\ ses-meg\meg\sub-16_ses-meg_task-facerecognition_run-06_events.tsv, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-01_ filteredHighPassNone.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-01_filteredHighPass1.fif, E:\Evgenii_Kalenko vich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-02_filteredHighPassNone.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduc tion\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-02_filteredHighPass1.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\ sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-03_filteredHighPassNone.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-fa cerecognition_run-03_filteredHighPass1.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-04_filteredHighPassNone.fi f, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-04_filteredHighPass1.fif, E:\Evgenii_Kalenkovich\reproducing-reprod 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ing\sub-12\ses-meg\meg\sub-12_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-13\ses-meg\meg\sub-13_ses-meg_task-facerecognition _epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-14\ses-meg\meg\sub-14_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reprod ucible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-15\ses-meg\meg\sub-15_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocess ing\sub-16\ses-meg\meg\sub-16_ses-meg_task-facerecognition_epoCleaned.fif jobid: 0 Job counts: count jobs 1 all 15 clean_epochs 16 ```

    Admittedly, there are too many input files in rule all most of which are not necessary. But even clean_epochs is hard to read.

Solution ideas:

  1. For the templates: use a hierarchy of templates and .format(x=???) so that we don't have som much repeating code. The higher-level templates should have very telling names like base_template_for_run_level_files. Maybe something else. Maybe not repeating ourselves is a bad idea here and explicitly writing out paths is better, IDK.
  2. For the output: let's change the working directory to the BIDS folder or, maybe, its parent and use relative path throughout where neceessary. The paths would still be very long but, I think, it would still help with readability.
kalenkovich commented 3 years ago

This is all too complicated for me. Maybe later.