Edition: workshop - March 25th 2025

nf-team

Alex
Valcourt Caron

Manon
Edde

Anthony Gagnon

Stanislas
Thoumyre

preprocessing

stats

analysis

quality control

Pipeline

#! /usr/bin/env bash
# preprocessing.sh

dwidenoise ${opts_dwidenoise} ${inputs_dwidenoise}

n4 ${opts_n4} ${inputs_n4}

bet ${opts_bet} ${inputs_bet}

crop ${opts_crop} ${inputs_crop}

#! /usr/bin/env bash
# preprocessing.sh

few subjects

same environment

just for one time

many subjects

reproducible

portable

really long

...

Documentation

CI-Testing

Stable Releases

Runs anywhere

Open Source

Package software

SIG: Special Interest Groups

Writing best practices for nf-core pipeline usage.
Creating and extending nf-core pipelines, as necessary.
Working together to harmonise usage of data formats.

NEUROIMAGING

main concepts

preprocessing

stats

analysis

quality control

#! /usr/bin/env bash
# preprocessing.sh

dwidenoise ${opts_dwidenoise} ${inputs_dwidenoise}

n4 ${opts_n4} ${inputs_n4}

bet ${opts_bet} ${inputs_bet}

crop ${opts_crop} ${inputs_crop}
....

channel
module
subworflow
workflow or pipeline

+ 50 modules

15 categories

9 subworkflows

3 pipelines in dev

nf-tractoflow, nf-pediatric, nf-mouseflow

Proposition, vision, goal for the library

Easy to setup

Easy to develop

Easy to use