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Questions - nextflow

Nextflow with Docker -- Problem with permission rights in WSL2

On WSL2 I am running the below Nextflow process via: script.nf -with-docker memesuite/memesuite:latest Outcome: Command error: .command.sh: line 2: foo.txt: Permission denied …but only when runnin...
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ATpoint

docker

wsl-2

nextflow

Votes: 0

Answers: 1

Latest Answer

You might need to play around with some of the docker scope config options, but, to answer your immediate question, you might need something like this in your nextflow.config: docker { enabled = t...
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Steve

Passing files to a Nextflow process based on a group ID

I am struggling with an issue that, probably, has a very basic solution. In my (dsl2) nextflow workflow, I have a number of processes that output a tuple of a file and a value, which indicates the gro...
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AGarofoli

groovy

nextflow

Votes: 0

Answers: 1

Latest Answer

One solution, which is perhaps the 'basic' solution you may have been working towards, is to mix your process outputs and then call the groupTuple operator, specifying the index of the element to be u...
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Steve

nextflow's process don't chain, stops after first success

I'm working on a colleague's pipeline Nextflow 19.04 and i have a weird behavior. in every case i used it, it was working like intended but recently we changed the technology of input data without mod...
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ul.Duc

nextflow

Votes: 0

Answers: 2

Latest Answer

Process execution stops if one or more input channels are empty. It's likely your input channel declared here is empty: bampbi_ch = bamtuple_ch.join(pbituple_ch).combine(init_ch) This could be becaus...
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Steve

How do I print nextflow script parameters in arparse style?

I would like to print the parameters of my nextflow script as a help menu (e.g., nextflow run main.nf --help), similar to the way arparse does it in python (i.e., script --help). I have trawled the we...
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user3479780

command-line-interface

argparse

nextflow

Votes: 0

Answers: 1

Latest Answer

There's no builtin for this, but if your params are only simple values something like the following might suffice: nextflow.enable.dsl=2 params.publish_dir = System.getenv('TMPDIR') ?: './results' p...
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Steve

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