clean the paths #8

kalenkovich · 2021-07-27T11:59:20Z

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

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')
 ```

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
 ucible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-01\ses-meg\meg\sub-01_ses-meg_task-facerecognition_run-05_filteredHighPassNone.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivati
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 _epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-06\ses-meg\meg\sub-06_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reprod
 ucible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-07\ses-meg\meg\sub-07_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocess
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 ucible\01_reproduction\data\bids\derivatives\01_preprocessing\sub-11\ses-meg\meg\sub-11_ses-meg_task-facerecognition_epoCleaned.fif, E:\Evgenii_Kalenkovich\reproducing-reproducible\01_reproduction\data\bids\derivatives\01_preprocess
 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:

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.
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.

The text was updated successfully, but these errors were encountered:

kalenkovich · 2021-10-05T21:59:38Z

This is all too complicated for me. Maybe later.

kalenkovich added the must label Sep 21, 2021

kalenkovich removed the must label Oct 5, 2021

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clean the paths #8

clean the paths #8

kalenkovich commented Jul 27, 2021 •

edited

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kalenkovich commented Oct 5, 2021

clean the paths #8

clean the paths #8

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kalenkovich commented Jul 27, 2021 • edited Loading

kalenkovich commented Oct 5, 2021

kalenkovich commented Jul 27, 2021 •

edited

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