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Remove name from conda environment.yml #5836

Closed
Tracked by #5828
ewels opened this issue Jun 19, 2024 · 1 comment
Closed
Tracked by #5828

Remove name from conda environment.yml #5836

ewels opened this issue Jun 19, 2024 · 1 comment
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@ewels
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ewels commented Jun 19, 2024

The conda environment.yml files that we use currently define a name attribute:

name: multiqc
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bioconda::multiqc=1.22.2

These were added in #4327 to fix an issue that we had cropping up with pytest-workflow for nf-core/sarek (see #4234):

ERROR ~ Error executing process > 'NFCORE_SAREK:sarek:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException

This seems to be due to a problem in conda with concurrent parallel environment creation (not present when using mamba). See nextflow-io/nextflow#4464 (comment)

The problem with the environment names is that they affect the container URIs generated by Wave, and so Seqera Containers. This reduces the ability for caching and reuse.

As we move away from pytest-workflow to nf-test we can safely remove these and simply deprecate pytest-workflow. It's unclear how common the error is for end users. The above Nextflow comment suggests that it may happen for some users with shared Nextflow instances on HPC, though these are probably relatively few in number and can be easily overcome by using mamba instead.

@ewels ewels linked a pull request Jun 19, 2024 that will close this issue
@ewels
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ewels commented Sep 6, 2024

Done in #6600 and nf-core/tools#3161

@ewels ewels closed this as completed Sep 6, 2024
@ewels ewels self-assigned this Sep 8, 2024
@famosab famosab mentioned this issue Nov 1, 2024
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