fastp version update?

[didiowen]

Description of the bug

Hi everyone,

I'm new to this workflow / pipeline and had just installed the latest version of nextflow. I was trying to run nextflow run nf-core/viralrecon -profile conda but I ran into the following error message:

WARN: There's no process matching config selector: .*:.*:PREPARE_GENOME:UNTAR_.*
WARN: Task runtime metrics are not reported when using macOS without a container engine
ERROR ~ Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (2)'

Caused by:
  Failed to create Conda environment
    command: conda create --mkdir --yes --quiet --prefix /Users/*****/bioinfo/work/conda/env-5f3a7d0793e009f164e4d72933b51818 bioconda::fastp=0.23.2
    status : 1
    message:
      Channels:
       - conda-forge
       - bioconda
       - defaults
      Platform: osx-arm64
      Collecting package metadata (repodata.json): ...working... done
      Solving environment: ...working... failed

I've tried conda install fastp=0.23.2 it seems that version 0.23.2 is no longer available (at least from my macOS arm64). Is there any way to work around this?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[Joon-Klaps]

Hi, yes this can be easily fixed. I'll make a PR for it. Within nextflow, you can modify the used environment by specifying a custom configuration file:

process {
    withName: 'FASTP' {
        conda "bioconda::fastp=0.23.4"
    }
}

And running it: nextflow run nf-core/viralrecon -profile conda,test -c my-custom-config.config --outdir test.

That said, viralrecon and all other nf-core pipelines use publicly available tools; not all tools will be compatible with ARM64 (through conda). Instead, running it with docker and specifying the arm profile will be easier than searching for ARM-compatible versions and patching all of them.

nextflow run nf-core/viralrecon -profile docker,arm,test --outdir test.