`nextflow` & `nf-core` on UPPMAX¶

https://www.nextflow.io

Official documentation: https://www.nextflow.io/docs/latest/index.html

Available versions from the module system¶

Check which versions are available

# On Pelle/Maya
module avail nextflow
-------------------------------------------------------- /sw/arch/eb/modules/all ---------------------------------------------------------
   Nextflow/24.10.2    Nextflow/25.10.2 (D)
...

# On Rackham/Bianca
module load bioinfo-tools
module avail nextflow
------------------------------------------------- /sw/mf/rackham/bioinfo-tools/pipelines --------------------------------------------------
   Nextflow/latest (D)    Nextflow/0.26.0     Nextflow/19.01.0         Nextflow/20.10.0         Nextflow/21.04.1    Nextflow/22.10.1
   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
   ...

Nextflow provided by the module system on Pelle and Maya do not allow users to alter the version as regular Nextflow installations.

`nextflow` from the module system on Rackham/Bianca¶

latest nextflow - Bianca/Rackham

module load bioinfo-tools
module load Nextflow/latest  # this also loads java as requirement

nextflow -v
nextflow version 25.04.7.5955

other nextflow versions on Rackham/Bianca

export NXF_VER=23.10.1

nextflow -v
nextflow version 23.10.1.5891

# To check the available versions on Rackham/Bianca
ls /sw/bioinfo/Nextflow/latest/rackham/nxf_home/framework/
20.04.1  21.04.3  22.10.1  22.10.4  23.04.2  23.10.0  24.04.2  24.04.5  24.10.2  24.10.5  25.04.1  25.04.4  25.04.7
20.07.1  21.10.6  22.10.2  22.10.8  23.04.3  23.10.1  24.04.3  24.10.0  24.10.3  24.10.6  25.04.2  25.04.5
20.10.0  22.10.0  22.10.3  23.04.1  23.04.4  24.04.1  24.04.4  24.10.1  24.10.4  25.04.0  25.04.3  25.04.6

`nf-core` from the module system¶

https://nf-co.re

Warning

On transit use module system is not available. Instead use the full path to the corresponding tools

nextflow - /sw/generic/pixi-tools/bin/nextflow
nf-core - /sw/generic/pixi-tools/bin/nf-core
dds-cli - /sw/generic/uv-tools/tool_bin/dds
pyega3 - /sw/generic/uv-tools/tool_bin/pyega3

# On Pelle/Maya
module load nf-core

# On Rackham/Bianca
module load bioinfo-tools
module load nf-core   # this also load the nextflow and java as requirements

`nf-core` pipelines on Bianca¶

Login to transit.uppmax.uu.se - documentation

Mount the wharf of your project.

user@transit:~$ mount_wharf sens2023531
Mounting wharf (accessible for you only) to /home/<user>/sens2023531
Password:
Second factor (TOTP UPPMAX):
done.

Navigate to your wharf folder

Disable Singularity cache

export SINGULARITY_DISABLE_CACHE=true
export APPTAINER_DISABLE_CACHE=true
unset NXF_SINGULARITY_CACHEDIR

Run /sw/generic/pixi-tools/bin/nf-core to download the pipeline.

 /sw/generic/pixi-tools/bin/nf-core pipelines download -c yes ampliseq

                                      ,--./,-.
      ___     __   __   __   ___     /,-._.--~\
|\ | |__  __ /  ` /  \ |__) |__         }  {
| \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                      `._,._,'

nf-core/tools version 3.0.2 - https://nf-co.re

WARNING  Could not find GitHub authentication token. Some API requests may fail.
? Select release / branch: 2.11.0  [release]

In addition to the pipeline code, this tool can download software containers.
? Download software container images: singularity

Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote
Singularity images are stored. This allows downloaded images to be cached in a central location.

? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n

If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: none
INFO     Saving 'nf-core/ampliseq'
        Pipeline revision: '2.11.0'
        Use containers: 'singularity'
        Container library: 'quay.io'
        Output directory: 'nf-core-ampliseq_2.11.0'
        Include default institutional configuration: 'True'
INFO     Downloading centralised configs from GitHub
INFO     Downloading workflow files from GitHub
INFO     Processing workflow revision 2.11.0, found 30 container images in total.
...

Running on Bianca

module load bioinfo-tools Nextflow
nextflow run ... -profile uppmax --project sens-XXXX-XX ....

Note: you might need -c configs/conf/uppmax.config, make sure you have the file (it is an option to download it during the pipeline download process). https://github.com/nf-core/configs/blob/master/conf/uppmax.config https://nf-co.re/configs/uppmax

`nf-core` pipelines available offline on Bianca/Maya¶

UPPMAX does not maintain complete mirror anymore. Only most requested pipelines are mirrored offline. To check the available pipelines, run

tree -L 2 /sw/bioinfo/nf-core-pipelines/latest/rackham

...
├── rnaseq
│   ├── 1.0
│   ├── 1.1
│   ├── 1.2
│   ├── 1.3
...

To run a pipeline from the UPPMAX mirror, run

module load bioinfo-tools
module load nf-core-pipelines # this also loads Nextflow

nextflow run $NF_CORE_PIPELINES/pipeline_name/revision/workflow ...

Common problems¶

Task is running out of resources (memory or time)

Add lines to your configuration that overrides the settings for the problematic task, for example:

process {
    withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
        cpus   = 12
        memory = '72.GB'
        time   = '24.h'
    }
}

More: https://www.nextflow.io/docs/latest/config.html#process-selectors

nextflow & nf-core on UPPMAX¶

Available versions from the module system¶

nextflow from the module system on Rackham/Bianca¶

nf-core from the module system¶

nf-core pipelines on Bianca¶

nf-core pipelines available offline on Bianca/Maya¶