NXF_WORK ignored

[Sasha Mikheyev]

Hello!

I can't get the NXF_WORK feature to change the 'work' path -- it is always created in the same directory as the script. I tried to change it using the nextflow.config, as below, without success

env { NXF_WORK = './data/work'
}

This verifiably changes the variable in the .nf file, but not the location of the working directory. Interestingly, using the -w switch with nextflow does change work directory. Any ideas?

Thank you,

Sasha

[Paolo Di Tommaso]

The env variables defined in the nextflow config file are meant to be used by the tasks executed by NF, not by the NF process itself. 

However you can still define the work directory in the config file by using the setting `workDir` eg. 

workDir = '/some/work/path`

Hope it helps. 

Cheers,
Paolo

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[Sasha Mikheyev]

Thank you very much!

Sasha

On Wednesday, 14 June 2017 18:10:31 UTC+10, Paolo Di Tommaso wrote:

The env variables defined in the nextflow config file are meant to be used by the tasks executed by NF, not by the NF process itself. 

However you can still define the work directory in the config file by using the setting `workDir` eg. 

workDir = '/some/work/path`

Hope it helps. 

Cheers,
Paolo

On Wed, Jun 14, 2017 at 4:14 AM, Sasha Mikheyev <mikh...@gmail.com> wrote:

Hello!

I can't get the NXF_WORK feature to change the 'work' path -- it is always created in the same directory as the script. I tried to change it using the nextflow.config, as below, without success

env { NXF_WORK = './data/work'
}

This verifiably changes the variable in the .nf file, but not the location of the working directory. Interestingly, using the -w switch with nextflow does change work directory. Any ideas?

Thank you,

Sasha

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