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Nextflow

For the demonstrator

  • Working directory is /nesi/project/nesi99999/Dinindu/20230503-pfr-demo/nextflow/

  • Content of /example_1 directory is 

    main.nf  Makefile  nextflow.config  nf-clean.sh

    • If any of the files are missing, download them from the repo

  • Content of /example_2 directory is 

    local_config/nesi_mahuika.config  nf_launch.sh

Example 1
  • Objective is to create the directory /output, populate it with three files bar.txt baz.txt foo.txt where the content of each file is a single string matching the filename
  • Launching the workflow can be done with 
    $ module load Nextflow/22.10.3 

$ nextflow run main.nf

It's interactive

  • Similar to other some workflow management systems, executing nextflow run main.nf will launch it as an interactive process. Therefore, it has to be launched as a background process with a utility such as tmux , screen , nohup.
  • OR....use Slurm's wrap function which is much better than above options 😊
  • Therefore, best way to launch is

code

sbatch --wrap 'nextflow run main.nf'
  • Check the status with

code

#OR use `squeue -j JOBID`
squeue --me

Can use nextflow tower

No restrictions (firewall rules,etc) with respect to using nf tower. As long as the TOWER_ACCESS_TOKEN is defined on current session ( Ideally add it to ~/.bashrc), tower can be called as usual via -with-tower flag and runtime information will be propagated to https://tower.nf/ 

sbatch --wrap 'nextflow run main.nf -with-tower'

Example 2
  • This is using the "image segmentation and extraction of single cell expression data" pipeline provided by nf-core https://nf-co.re/imcyto/1.0.0
  • Given this is a Singularity container based workflow, it required few variables such as SINGULARITY_BIND. Ideal approach is to prepare a launch script as below and then submit it with sbatch

#!/bin/bash -e

#Can use Apptainer as well
module purge
module load Singularity       
module load Nextflow/22.10.3


#Singularity and Nextflow variables
export SINGULARITY_BIND="/nesi/project,nesi/nobackup,/opt/nesi"
export SINGULARITY_TMPDIR=/nesi/nobackup/nesi99999/Dinindu/cache
export SINGULARITY_CACHEDIR=$SINGULARITY_TMPDIR
setfacl -b "$SINGULARITY_TMPDIR"
setfacl -b "/nesi/project/nesi99999/Dinindu/20230503-pfr-demo/nextflow/example_2"

export NXF_EXECUTOR=slurm
export NXF_SINGULARITY_CACHEDIR=$SINGULARITY_CACHEDIR

srun nextflow run nf-core/imcyto -profile test,singularity \
-c local_config/nesi_mahuika.config  -resume -with-tower
- Submit the script with sbatch nf_launch.sh