speechmetryflow

Running

nextflow run lingualab/speechmetryflow -r 0.0.2 --input participant_ids.csv

Replace the -r option with the release you want to use

Files needed

participant_ids.csv

This CSV file must contain at least 3 columns:

• participant_id is required for the pipeline to find your files. These files must begin by the participant_id. To specify the folder where your files are located, see nextflow.config.
• language: 2 choices, en or fr.
• sex: 2 choices, male or female.

Example:

participant_id	language	sex
sub-PKM8767	en	male
sub-SBK4467	en	female

nextflow.config

Example for elm server:

params {
    audio_folder = "/data/brambati/dataset/CCNA/derivatives/audio_extract"
    text_folder = "/data/brambati/dataset/CCNA/derivatives/cookie_txt"
}

process {
    container = "/data/brambati/local/containers/lingualab/speechmetryflow_0.0.2.sif"
}

apptainer {
    runOptions = "-B /data/brambati"
}

executor {
    cpus = 20
}

output

The pipeline produces 3 csv files:

• population_audio_metrics: metrics compute with lingualabpy_audio_metrics from lingualabpy
• population_uhmometer_metrics: metrics compute with uhm-o-meter
• population_text_metrics: metrics compute with Text2Variable

Metrics description