Running nf-core pipelines/ Nextflow on Rackham and Bianca

The nf-core pipelines are not supported anymore at UPPMAX. To learn how to download your pipeline for offline use on Bianca, please follow this tutorial nf-core pipelines on Bianca instead.

• Running nf-core pipelines/ Nextflow on Rackham and Bianca
  • 1. Available modules
  • 2. Test: Running sarek v3.1.2
  • 3. Troubleshooting
  • Contacts:

1. Available modules

i. Load the bioinfo-tools module tree

$ module load bioinfo-tools

ii. Related modules and versions as of 2023.04.24

$ module avail Nextflow
-------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines ---------------------------------------------------
   Nextflow/latest    Nextflow/0.26.0     Nextflow/19.01.0         Nextflow/20.10.0         Nextflow/21.04.1    Nextflow/22.10.1 (D)
   Nextflow/0.17.3    Nextflow/0.31.1     Nextflow/20.02.0-edge    Nextflow/21.01.0-edge    Nextflow/21.10.6
   Nextflow/0.22.2    Nextflow/18.10.1    Nextflow/20.04.0-edge    Nextflow/21.02.0-edge    Nextflow/22.10.0

$ module avail nf-core/
-------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines ---------------------------------------------------
   nf-core/latest    nf-core/1.12.1    nf-core/1.14    nf-core/2.1    nf-core/2.4.1    nf-core/2.6 (D)

$ module avail nf-core-pipelines
-------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines ---------------------------------------------------
   nf-core-pipelines/latest

Load the nf-core-pipelines module. The module will load the correct versions for Nextflow, java, and nf-core automatically.

$ module load bioinfo-tools  nf-core-pipelines

$ module list 
Currently Loaded Modules:
  1) uppmax   2) bioinfo-tools   3) java/OracleJDK_11.0.9   4) Nextflow/22.10.0   5) nf-core-pipelines/latest

If you want, after this you can load the latest Nextflow version with module load Nextflow/latest

2. Test: Running sarek v3.1.2

For convenience, all stable versions of the official nf-core pipelines are mirrored locally and most of the required Singularity containers are also available.

Start an interactive job.

$ interactive -A nais2023-1-123 -p core -n 1 -t 10-00:00:00

Interactive jobs on Rackham and Bianca are running withing screen session, which ensures that the program will continue running even if you lose connection to the cluster or the session is closed because of inactivity in the shell.

$ nextflow run $NF_CORE_PIPELINES/sarek/3.1.2/workflow --project nais2023-1-123 -profile uppmax,test --outdir outdir

...
-[nf-core/sarek] Pipeline completed successfully-
Completed at: 24-Apr-2023 16:11:53
Duration    : 1h 38m 25s
CPU hours   : 0.1
Succeeded   : 26

Have a look at https://github.com/nf-core/configs/blob/master/docs/uppmax.md for detailed instructions on running nf-core on UPPMAX and hints on additional options. Note the small difference when loading the modules.

https://github.com/nf-core/configs/blob/master/conf/uppmax.config details on the predefined uppmax profile.

3. Troubleshooting

Check that you have somewhat reasonable environment before running nextflow.

$ env | grep 'NXF_\|NF_'

NXF_HOME=/home/USER/.nextflow
NXF_TEMP=/scratch/USER
NXF_SINGULARITY_LIBRARYDIR=/sw/bioinfo/nf-core-pipelines/latest/rackham/singularity_cache_dir
NXF_LAUNCHER=/scratch
NXF_DIST=/sw/bioinfo/Nextflow/22.10.0/rackham/nxf_home/framework
NF_CORE_PIPELINES=/sw/bioinfo/nf-core-pipelines/latest/rackham
NF_CORE_PIPELINES_ROOT=/sw/bioinfo/nf-core-pipelines/latest/rackham

Check that you have space to run the calculations.

$ uquota

Your project     Your File Area       Unit        Usage  Quota Limit  Over Quota
---------------  -------------------  --------  -------  -----------  ----------
home             /home/USER           GBytes       10.2         32.0            
home             /home/USER           Files      165979       300000            
naiss2023-22-21  /proj/introtouppmax  GBytes        3.7          128            
snic2022-5-301   /proj/snic_ae        GBytes        0.0          128            

Contacts:

• Pavlin Mitev
• UPPMAX
• AE@UPPMAX - related documentation

tags: UPPMAX,nextflow,nf-core