DSL1 legacy code in is not working with Nexflow >25

[MPourjam]

Nextflow >25 has apparently removed the support for DSL1 syntax and throws error. For example: pipelines/metagenomic/metagenomic.nf:608

I tried with latest Nextflow 24 but then nextflow fails to create environment when using mamba or conda:

Caused by:
  Failed to create Conda environment
    command: mamba create --mkdir --yes --quiet --prefix /media/adminuser/MSD-Storage/Mohsen/TACTIC_Benchmark/CAMISIM/work/conda/env-80eceaba5338f1a2a39ebae57705ef62 conda-forge::biopython=1.83 conda-forge::python=3.11.5
    status : 109
    message:
      The following argument was not expected: --mkdir
      Run with --help for more information.

mamba version 2.4.0 does not support --mkdir argument.

and when I use conda:

Caused by:
  Failed to create Conda environment
    command: conda create --mkdir --yes --quiet --prefix /media/adminuser/MSD-Storage/Mohsen/TACTIC_Benchmark/CAMISIM/work/conda/env-80eceaba5338f1a2a39ebae57705ef62 conda-forge::biopython=1.83 conda-forge::python=3.11.5
    status : 2
    message:
      usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
      conda: error: unrecognized arguments: --mkdir

My environment files:

CAMISIM.tar.gz

[MPourjam]

The changes below made the pipeline work for metagenomics simulation:

• metagenomics.nf.patch: This resolved the issue I had with nextflow >25
• metatranscriptomics.nf.patch: This resolved probable errors with nextflow >25

DSL2_patches.zip

[AlphaSquad]

Hi, thank you for bringing this to our attention and to propose a fix already! I will have a look and hope to include it soon