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Nextflow materials
Contributors Persona 1: Sarah Bonnin, Toni Hermoso Pulido, Renuka Kudva, Tuur Muyldermans, Maxime Garcia
Contributors Persona 2: Luca Cozzuto, Jose Espinosa-Carrasco, Maxime Garcia
Nextflow users (persona 1)
Nextflow users (more introductory - concepts why - exercises explaining fundamentals)
Learner's profiles
Who are they?
What problem are they having?
How will the tutorial/workshop help them?
Learner's objectives
*Goals: “After following one of these tutorials, learners will be able to …”
Training materials
Example pipeline: https://github.com/nextflow-io/rnaseq-nf Tutorial based on this pipeline (focus on how to edit & construct the pipeline): https://github.com/cbcrg/nf-phdcourse20
Outline:
Introduction nextflow and language (theoretical)
Knowing where to find a pipeline (github, nf-core, …) and which one to use.
Import a pipeline (download/clone locally or from github - but also possible to pull (nextflow pull)) - focus on DSL2 pipelines. https://github.com/nextflow-io/awesome-nextflow
(Exercise difference between
nextflow run/pull
andgit clone
.) The latter is for later when we need to change the profiles in config.nextflow run nextflow-io/rnaseq-nf
nextflow pull nextflow-io/rnaseq-nf -r v1.2
(Pull a given version)nextflow pull nextflow-io/rnaseq-nf -r master
(Pull latest from master branch)nextflow pull nextflow-io/rnaseq-nf -r 98ffd10a76
(Pull a given commit)Exercise: nextflow-pull a specific pipeline (they need to find themselves). Extra: define release (or tag/release/commit)
Execute a pipeline
<pipeline>
(toy pipelines = tiny pipelines) + fast, easy, simple. When more familiar → then go to a nf-core pipeline.nextflow run nextflow-io/rnaseq-nf
Side note: If you don't do nextflow pull, so immediately nextflow run, it will also fetch it from the internet (github)
Sidenote: Error:
Command error: .command.sh: line 2: salmon/fastqc/multiqc: command not found
. Due to tools not being installed. Fix with conda or docker.Conda:
conda env create -f conda.yml
&conda activate rnaseq-nf
Docker: (if docker installed):
nextflow run nextflow-io/rnaseq-nf -with-docker
Singularity: (if Singularity installed):
nextflow run nextflow-io/rnaseq-nf -with-singularity
Locate and describe the output after running a pipeline → workdir with different files (.command.*).
Run with different parameters: nextflow-specific versus pipeline-specific (- vs –)
params.<name>
on runtime:nextflow run nextflow-io/rnaseq-nf --reads path/to/reads
(e.g. with only part of the reads:ggal/ggal_liver_{1,2}.fq
)Explain config files and being able to do minor modifications (eg. change version of docker container, parameters like computation power)
Extra:
Nextflow pipeline developers (persona 2)
Learner's profiles
Learner's objectives
Prerequisites for the course/tutorial
Define exercises with learning outcomes (measurable)*
*Goals: “After following one of these tutorials, learners will be able to …”
Training materials
Outline:
Contribution notes
This Markdown-file can be collaboratively and simultaneously edited from this link.
Please push to the branch
nextflow
in order not to make conflicting versions. This is automatically done when you push the Hackmd-file to GitHub (click on Settings… right top –> Versions and GitHub Sync –> Push). However, might only be done by @tmuylder.