Calculation Module (CLI)

Contents

Calculation Module (CLI)#

Step 0 (recommended): create editable config file(s)#

Export package defaults to your working directory first:

mkdir -p /path/to/configs
get-megqc-config --target_directory /path/to/configs --filename settings_global.ini

For multi-dataset runs with dataset-specific settings:

get-megqc-config --target_directory /path/to/configs --filename ds1.ini
get-megqc-config --target_directory /path/to/configs --filename ds2.ini

Edit the copied files as needed. Keep package defaults unchanged.

Step 1: minimal calculation run#

run-megqc \
  --inputdata /path/to/dataset \
  --config /path/to/configs/settings_global.ini

Common controls#

--subs 001 002 003
--n_jobs 4
--derivatives_output /path/to/derivatives_root
--analysis_mode legacy|new|reuse|latest
--analysis_id <id> (required with reuse)
--existing_config_policy provided|latest_saved|fail
--processed_subjects_policy skip|rerun|fail

Multi-dataset examples#

A) Same config for all datasets#

run-megqc \
  --inputdata /path/ds1 /path/ds2 /path/ds3 \
  --config /path/to/configs/settings_global.ini \
  --n_jobs 6

B) Per-dataset subjects and per-dataset configs#

run-megqc \
  --inputdata /path/ds1 /path/ds2 \
  --subs_per_dataset \
    "/path/ds1::001,002,003" \
    "/path/ds2::all" \
  --config_per_dataset \
    "/path/ds1::/path/to/configs/ds1.ini" \
    "/path/ds2::/path/to/configs/ds2.ini" \
  --n_jobs 4

C) Profile-based new run for sensitivity tracking#

run-megqc \
  --inputdata /path/dataset \
  --config /path/to/configs/settings_global.ini \
  --analysis_mode new \
  --analysis_id qa_pass_01 \
  --existing_config_policy provided \
  --processed_subjects_policy skip

Run ALL (calculation + plotting in one command)#

If --run-all is used, calculation is executed first, then plotting scopes are executed.

All plotting scopes#

run-megqc \
  --inputdata /path/ds1 /path/ds2 \
  --config /path/to/configs/settings_global.ini \
  --run-all --all

Selective plotting scopes#

run-megqc \
  --inputdata /path/ds1 /path/ds2 \
  --config /path/to/configs/settings_global.ini \
  --run-all \
  --qa-subject --qa-group --qc-group

Output layout#

legacy mode: /path/dataset/derivatives/Meg_QC/
profile mode: /path/dataset/derivatives/Meg_QC/profiles/<analysis_id>/

Use run-megqc --help for the complete flag reference.