Nextflow Hackathon

Joint Morning Session: Nextflow 101 (joint, Boehm SR, 9:30-12:30)

Goal: Understand structure of nf-file and key concepts (Channels, Processes, Operators)

Reference: https://training.nextflow.io/basic_training/intro/

practical work through intro (hello_world.nf)
customisation and adaptation
- add parameters: e.g. params.name ("Hello $name")
- add processes: to print "uname -a and process-ID"
- process directives: - [ ] control processes locally and globally (cpus, memory, container) - [ ] use container from dockerhub (global or process-wise)
configuration: run on slurm
workflow on github and test

  nextflow run  github.com/maxplanck-ie/testflow --params ... -with-apptainer

Lunch (12:30 - 13:30): Pizza @ Boehm SR

Make your selection here: https://pizzamonalisa.de

Afternoon (13:30:15:30): Real Workflows

Goals:

employ other workflows with singularity, locally and with slurm (queue test)

Group 1: Epi2Me, wf_alignment (DNA)

Challenge: Can we make this work with singularity and slurm?

Input: basecalled BAM (downsampled, drosophila)
Output: alignment BAM + QC
run wf_alignment (dm6) with apptainer (identify approrpiate container)
Extensions?
- add process (e.g. samtools flagstat)
- send email upon completion

Group 2: nf-core, nanoseq (RNA)

Challenge: Can we predict RNA modifications? (--> m6anet; skip all other analyses)

Input: samplesheet.csv, pod5/fast5 (subsampled)
Output: methylation calls: data.result.csv.gz

Final Meeting (16:00): Boehm SR

exchange workflows, test runs & final discussion

Examples

module load nextflow/23.10.0 
nextflow run -with-apptainer docker://ubuntu:20.04 sources/tutorial.nf 

# test runs without modification calling
nextflow run nf-core/nanoseq -profile test,singularity

# couldn't get to work
nextflow run ~/.nextflow/assets/epi2me-labs/wf-alignment  --bam data/bam --references /data/repository/organisms/dm6_flybase_r6.12/genome_fasta -with-singularity ontresearch/wf-alignment -without-docker

TobiasHohl/nextflow_hackathon