Problems using Nextflow to run NanoRtax Pipeline

Nextflow Help
1

Hello! I am trying to run this pipeline called NanoRtax (GitHub - genomicsITER/NanoRTax: Real-time analysis pipeline for nanopore 16S rRNA data) 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!

2

Nextflow DSL1 is no longer supported in recent versions of Nextflow. According to the output you shared, you’re running Nextflow 23.10.1, a stable version released at the end of 2023. The option you have (apart from converting the pipeline to DSL2 :sweat_smile:) is to run Nextflow in a 22.10.x version. You can do that with the following command:

NXF_VER=22.10.1 nextflow run main.nf --reads ‘home/irodriguez1/cquinones/fastq_pass/barcode01/AQG952_pass_barcode01_eb363db4_310c5cba_0.fastq’ -profile conda