Setting workDir in nextflow.config?

[Eric 'Siggy' Scott]

Hello NextFlowers,

Is there a way to set the workDir inside nextflow.config?

I understand that I can use the -w option or the NXF_WORK variable.  But I'd prefer to set everything in one config file (instead of an external script).

I've tried the following, but it seems to have no effect:

workflow.workDir = '/scratch/user/work/'

env.NXF_WORK = '/scratch/user/work/'

Thanks,

Siggy

--

——

Eric "Siggy" Scott | MITRE

Senior Artificial Intelligence Engineer, T831: AI & Autonomous Systems Dept.

Doctoral Candidate, George Mason University

http://mason.gmu.edu/~escott8/

[Paolo Di Tommaso]

Yes, just 

```

workDir = 'something'

```

p

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[Eric 'Siggy' Scott]

Perfect—thanks, Paolo!

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[Anand Venkatraman]

Is there a way to set this within a main.nf file

Something like

params.in = './my_input'
params.outdir = "s3_path"

I cannot do params.work-Dir

On Thursday, February 6, 2020 at 8:52:52 AM UTC-5, Paolo Di Tommaso wrote:

Yes, just 

```

workDir = 'something'

```

p

On Wed, Feb 5, 2020 at 10:36 PM Eric 'Siggy' Scott <esc...@gmu.edu> wrote:

Hello NextFlowers,

Is there a way to set the workDir inside nextflow.config?

I understand that I can use the -w option or the NXF_WORK variable.  But I'd prefer to set everything in one config file (instead of an external script).

I've tried the following, but it seems to have no effect:

workflow.workDir = '/scratch/user/work/'

env.NXF_WORK = '/scratch/user/work/'

Thanks,

Siggy

--

——

Eric "Siggy" Scott | MITRE

Senior Artificial Intelligence Engineer, T831: AI & Autonomous Systems Dept.

Doctoral Candidate, George Mason University

http://mason.gmu.edu/~escott8/

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[Paolo Di Tommaso]

Nope. The work dir can set via `-w` command-line option, NXF_WORK env variable and the `workDir` setting in the configuration file. 

Hope it helps 

p

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[Sayantan Das]

Hi Paolo,

How to have a variable in the workDir option inside the config file ? 

Something like ? Thank you so much for your help. 

scratch/\$(whoami)/

[Paolo Di Tommaso]

```

workDir  = "/some/path/${my_variable}"

```

Hope it helps 

p