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.shfew 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
nf-neuro_workshop_March_2025
By Arnaud Boré
