Nextflow version 0.26 Installation

[Behnaz]

Hi everyone

I'm trying to run a Nextflow-based pipeline, but I receive this message: "This workflow requires Nextflow version 0.26 or greater -- You are running

version 20.01.0"

I have tried two commands to install Nextflow on my system: wget -qO- https://get.nextflow.io | bash AND curl -fsSL get.nextflow.io | bash

?Both of them install version 20.01.0. What should I do to get version 0.26

Thank you for your help

[Kevin Sayers]

You can grab the binary (nextflow-0.26.0-all) from: https://github.com/nextflow-io/nextflow/releases/tag/v0.26.0 

You can also run a specific version of Nextflow using "NXF_VERSION=0.26.0 nextflow run ...." and it will automatically pull the correct version of Nextflow

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[Theo]

Just to add that on the provided link there are 2 files the nexflow that will download and self "compiled" and the nexflow-0.26.0-all that is ready. just rename that one to a simple nextflow and you are good to go.

[Behnaz]

Thank you Sayerskt and Theo for your responses

  Based on what I understood, I removed my last version of Nextflow, downloaded nextflow-0.26.0-all, renamed it to nextflow, and ran the pipeline by writing NXF_VERSION=0.26.0 nextflow run 

But again I got the same message. Have I done something wrong?

در جمعه 20 مارس 2020، ساعت 13:47:02 (UTC+11)، Behnaz نوشته:

[Paolo Di Tommaso]

What is the output of the following command?: 

NXF_VERSION=0.26.0 nextflow info

p

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[Theo]

 Just to add that I remember I had some .nx* leftovers that were forcing the nextflow to reupdate?

In addition to what Paolo asked for, doa ls -a and take a look at the output.

Also had something similar.

Best

[Behnaz]

Here it is:

Version: 20.01.0 build 5264

I just remembered that I had put Nextflow version 20.01.0 in my PATH, so I removed and replaced it by the downloaded version 0.26.0. But this time when I ran nextflow info command, I receive a new error:

 

readlink: illegal option -- f

usage: readlink [-n] [file ...]

ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 is installed

I already have Java version 13.0.2. Do you think I need to install Version 8? 

On Mon, Mar 23, 2020 at 1:27 AM Behnaz <bkh...@gmail.com> wrote:

Thank you Sayerskt and Theo for your responses

  Based on what I understood, I removed my last version of Nextflow, downloaded nextflow-0.26.0-all, renamed it to nextflow, and ran the pipeline by writing NXF_VERSION=0.26.0 nextflow run 

But again I got the same message. Have I done something wrong?

در جمعه 20 مارس 2020، ساعت 13:47:02 (UTC+11)، Behnaz نوشته:

Hi everyone

I'm trying to run a Nextflow-based pipeline, but I receive this message: "This workflow requires Nextflow version 0.26 or greater -- You are running

version 20.01.0"

I have tried two commands to install Nextflow on my system: wget -qO- https://get.nextflow.io | bash AND curl -fsSL get.nextflow.io | bash

?Both of them install version 20.01.0. What should I do to get version 0.26

Thank you for your help

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[Paolo Di Tommaso]

Yes

  

I already have Java version 13.0.2. Do you think I need to install Version 8? 

در سه‌شنبه 24 مارس 2020، ساعت

 

[Behnaz]

Thanks Thao

Interestingly, when I ran ls -a command in my Home directory, I had ten files named .nextflow.log, .nextflow.log.1, ..., .nextflow.log.9. Are these making a problem? How can I remove them?

در سه‌شنبه 24 مارس 2020، ساعت 7:55:04 (UTC+11)، Theo نوشته:

[Paolo Di Tommaso]

That are log files for debugging purpose. 

You can remove at any time. 

Have a look at  https://linuxconfig.org/bash-scripting-tutorial-for-beginners

p

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