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AlfredUg / QuasiFlow

A Nextflow Pipeline for Analysis of NGS-based HIV Drug Resistance Data
GNU General Public License v3.0
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Not able to run QuasiFlow #4

Open jpflorido opened 1 year ago

jpflorido commented 1 year ago

Hi, I'm trying to run QuasiFlow but the following error appears: Command error: .command.sh: line 3: trim_galore: command not found

through the following command: nextflow run ~/.nextflow/assets/AlfredUg/QuasiFlow --reads "$PWD/*_{1,2}.fastq" -profile conda

I'm running with Nextflow version 22.10.7.5853, miniconda latest version. It seems that the conda environment for installing the dependencies is not created and that's the main reason trim_galore is not found.

Any suggestions? Thanks, Javier

AlfredUg commented 1 year ago

Hi @jpflorido, Sure, seems like the conda environment is not created and as such trim_galore is not found. You could try inspecting your conda envs to confirm this. Otherwise, we are hoping to share a link to an updated docker image in the coming few days.