Problems with Nextflow to run NanoRtax Pipeline

Question

[kerianaleerivera]

Hello! I am trying to run this pipeline called NanoRtax (https://github.com/genomicsITER/NanoRTax) to analyze my nanopore 16s data, specifically I want to reach the diversity matrics. They provide a script called main.nf and apparently I just have to give it my fastq samples.

This pipeline is built using Nextflow. I managed to install Nextflow using a version of miniconda from 2020 that got provided by the performance computing facility of my institution.

This is the code I am writing on the command line:

nextflow run main.nf --reads 'home/irodriguez1/cquinones/fastq_pass/barcode01/AQG952_pass_barcode01_eb363db4_310c5cba_0.fastq' -profile conda

However I keep on getting this error:

N E X T F L O W  ~  version 23.10.1
Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

Any tips on how to fix this? I looked over the script and it is properly written in DSL2 syntax.

Thank you!

Answer 1

[bhumm]

After a brief look at the main.nf it does appear to still be using DSL1. You could try adding nextflow.enable.dsl = 1 to the script to see if it fixes the error. Another option is upgrading the script to DSL2, which might be tricky dependent on your comfort with Groovy. Finally, you could check your version of nextflow to ensure you are using Nextflow 22.10.x or earlier (you can use conda list nextflow or nextflow -version to check this while your environment is activated).

See this part of the nextflow documentation for more information on DSL migration.

Answer 2

[Pierre Lindenbaum]

DSL1 is not supported anymore, but you can always download+compile the NF that was released at the time of your DSL1 workflow : https://github.com/nextflow-io/nextflow/releases

Answer 3

[colindaven]

As the others have said, you need an older version of nextflow which still runs DSL1 (think v1 of nextflow) scripts. The current Nextflow DSL version is DSL2.

To fix this (if you have java installed) you can do this.

wget https://github.com/nextflow-io/nextflow/releases/download/v23.04.4/nextflow-23.04.4-all
mv nextflow-23.04.4-all nextflow
./nextflow

Or if you prefer conda you can just make sure you get the 23.04 version of nextflow to make sure it runs.

Sometimes java versions and nextflow versions don't get along too well either. I used to use Java 11.0.1 but know use Java16 successfully with the complete distribution, ie. listed in the wget command above.