Is it possible to use Nextflow with the `libmamba` conda solver?

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Hey, James!

Yes, you can. I can’t reproduce your error.

I did the following:

conda update -n base conda
conda install -n base conda-libmamba-solver
conda config --set solver libmamba

I confirmed with conda config --get solver, which returned --set solver libmamba. conda config --show also confirmed it, but much more verbose :laughing:

Then, I created a new folder and added the following Nextflow script:

process FOO {
  conda 'fastqc'
  debug true

  output:
  stdout

  script:
  """
  fastqc --version
  """
}

workflow {
  FOO()
}

Ran with NXF_VER=23.04.1 nextflow run main.nf -with-conda and got as output the following:

CAPSULE: Downloading dependency io.nextflow:nextflow:jar:23.04.1
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:23.04.1
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:23.04.1
Nextflow 23.10.0 is available - Please consider updating your version to it
dN E X T F L O W  ~  version 23.04.1
Launching `main.nf` [loving_cray] DSL2 - revision: e432c2850d
executor >  local (1)
[d2/28d2f3] process > FOO [100%] 1 of 1 ✔
Creating env using conda: fastqc [cache /Users/mribeirodantas/conda-test/work/conda/env-23037893fdd4cef8d4acc5fe82ba1899]
FastQC v0.12.1

PS: I tried running nextflow run nf-core/taxprofiler -profile conda,test -r 1.1.1 --outdir ./results as you did, and it works past the NFCORE_TAXPROFILER:TAXPROFILER:LONGREAD_HOSTREMOVAL:MINIMAP2_INDEX' step so for some reason I can’t reproduce this either.

[bf/e48529] process > NFCORE_TAXPROFILER:TAXPROFILER:LONGREAD_HOSTREMOVAL:MINIMAP2_INDEX                             [100%] 1 of 1 ✔

I didn’t wait for it to finish, though.

I would guess this issue is related to your conda version. I’m using v23.9.

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