changed 2 years ago  
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nextflow on Rackham and Bianca

Offline mirror of the stable nf-core-piplenes is available on Rackham and Bianca via

$ module load bioinfo-tools nf-core-pipelines/latest

This will load nextflow as requirement as well.
As it appears, some pipelines might need different version of nextflow to work, which is beyond what the software module system is capable to resolve.

Update 2023.06.20: nf-core-pipelines/latest now will load the latest version of nextflow. If you need to use different/older version of the tool you can switch by setting the environmental variable NXF_VER to one of the pre-installed.

You can check which versions are pre-installed:

$ ls /sw/bioinfo/Nextflow/latest/rackham/nxf_home/framework/

20.04.1  20.07.1  20.10.0  21.04.3  21.10.6  22.10.1  22.10.2  22.10.3  22.10.4  22.10.8  23.04.1  23.04.2

Example:

# Load nf-core-pipelines
$ module load bioinfo-tools nf-core-pipelines/latest

Nextflow not loaded, will load Nextflow

Note that NXF_HOME is set to $HOME/.nextflow
Please change NXF_HOME to a place in your project directory (export NXF_HOME=yourprojectfolder)

Please use   export NXF_VER=nextflow_version    to select different version
https://www.nextflow.io/docs/latest/config.html#environment-variables


# check nextflow version
$ nextflow -v
nextflow version 23.04.2.5870

# change the nextflow version using the internal version mechanism
export NXF_VER=22.10.8
$ nextflow -v
nextflow version 22.10.8.5859

Contacts:

tags: UPPMAX, nextflow
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