Conda Unable to Create Environment

[FrostFlow13]

Bug report

As some backing information, I encountered this bug during the Nextflow Training 2.1.3 Part 6 (https://training.nextflow.io/2.1.3/hello_nextflow/06_hello_config/). I am intending on using either Singularity/Apptainer containers or defined Conda environments, and this bug poses a problem for the Conda possibility and for the training.

Expected behavior and actual behavior

Expected behavior: Running nextflow run hello-config.nf in "Part 6 Section 1.3. Run the workflow to verify that it can use Conda" should result in successful execution of the workflow.

Actual behavior: Running nextflow run hello-config.nf in "Part 6 Section 1.3. Run the workflow to verify that it can use Conda" results in an error, failing to create a Conda environment.

Steps to reproduce the problem

All steps as-written in Nextflow Training 2.1.3.

Program output

(base) [...]:/srv/dev/nextflow_playground/training/hello-nextflow$ nextflow run hello-config.nf

 N E X T F L O W   ~  version 24.10.5

Launching `hello-config.nf` [distracted_roentgen] DSL2 - revision: e9e72441e9

executor >  local (7)
executor >  local (7)
[ce/031a4a] sayHello (1)       | 3 of 3 ✔
executor >  local (7)
[ce/031a4a] sayHello (1)       | 3 of 3 ✔
[ec/cda30b] convertToUpper (2) | 3 of 3 ✔
[38/d09c56] collectGreetings   | 1 of 1 ✔
[-        ] cowpy              -
There were 3 greetings in this batch
Creating env using conda: conda-forge::cowpy==1.1.5 [cache /srv/dev/nextflow_playground/training/hello-nextflow/work/conda/env-898314d566668b6587ad714ae06b8520]
ERROR ~ Error executing process > 'cowpy'

Caused by:
  Failed to create Conda environment
    command: conda create --mkdir --yes --quiet --prefix /srv/dev/nextflow_playground/training/hello-nextflow/work/conda/env-898314d566668b6587ad714ae06b8520 conda-forge::cowpy==1.1.5
    status : 2
    message:
      usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...
      conda: error: unrecognized arguments: --mkdir



 -- Check '.nextflow.log' file for details

.nextflow.log

Environment

• Nextflow version: [24.10.5]
• Java version: [openjdk version "17.0.10" 2024-01-16]
• Operating system: [Ubuntu 24.04.1 LTS]
• Bash version: [GNU bash, version 5.2.21(1)-release (x86_64-pc-linux-gnu)]

Additional context

After doing some digging, this may be related to the version of Conda I am running (Conda 25.3.0). According to the Release Notes (https://docs.conda.io/projects/conda/en/stable/release-notes.html#deprecations),

Remove conda create --mkdir. Redundant argument. (#14644)

I believe this error is related to Nextflow attempting to still use the "--mkdir" argument. Would there be any way to create a workaround, or should I attempt to install a version of Conda prior to 25.3.0?

[FrostFlow13]

Installing Conda 25.1.1 resulted in successful creation of the environment and a successful run of the code, further supporting the likelihood of an incompatibility with Conda 25.3.0.

[pditommaso]

Thanks for this troubleshooting. If I'm understanding correctly they have restored it in 4.6 stating this conda/conda#7211.

In this case the better thing to do it so add a warning in the docs. /cc @christopher-hakkaart

[danpal96]

According to: https://github.com/conda/conda/blob/3259a9c914446a44b12e7c4fa191972892b8e394/CHANGELOG.md#2530-2025-03-17
conda create --mkdir was removed for being redundant in 25.3.0 (2025-03-17) conda/conda#14644

[christopher-hakkaart]

Thanks @danpal96 , I'll double check this and update the docs accordingly.

[FrostFlow13]

I was working on a pipeline of my own, and I discovered that this issue also appears to be present for Mamba (2.1.0), where it also throws the error:

[...]
Failed to create Conda environment
command: mamba create --mkdir --yes --quiet --prefix /srv/dev/denovo_assembly_pipeline/work/conda/env-4b2cd02f7d6d162881d93d79c8e66d66 bioconda::fastp==0.24.0
status : 109
    message:
        The following argument was not expected: --mkdir

I have not yet tried older versions of Mamba, but unlike Conda I am not able to find a specific changelog note of Mamba removing --mkdir, but it could just be that I haven't dug far enough.

[christopher-hakkaart]

I've been testing this today and agree with @danpal96 that --mkdir was removed in 25.3.0.

It looks like it was a warning that it would be depreciated from 25.3.0 onwards. I can't see anything suggesting it would be added back.