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Newer nextflow version (26.04.x) import errors #251
Description
I think this may be a more general problem and not one limited to our systems... When running the egapx workflow with newer nextflow versions (26.04.1 build 12112, in this case), I was running into import errors. I ran:
echo "Running egapx"
eval "$(conda shell.bash hook)"
conda activate egapx
python /project/brant/mike-home/git/egapx/ui/egapx.py <yaml> -e singularity -w tmp -o <out>And the error was:
Error ../../../../../../ddnA/project/brant/mike-home/git/egapx/nf/subworkflows/ncbi/main.nf:6:1: Groovy `import` declarations are not supported -- use fully-qualified name inline instead
│ 6 | import groovy.yaml.YamlBuilder
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error ../../../../../../ddnA/project/brant/mike-home/git/egapx/nf/ui.nf:7:1: Module could not be parsed: '/ddnA/project/brant/mike-home/git/egapx/nf/subworkflows/ncbi/main.nf'
│ 7 | include { egapx } from './subworkflows/ncbi/main'
╰ | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^Reverting to an earlier version of nextflow fixed the issue:
echo "Running egapx"
eval "$(conda shell.bash hook)"
conda activate egapx
export NXF_VER=25.04.3
python /project/brant/mike-home/git/egapx/ui/egapx.py <yaml> -e singularity -w tmp -o <out>
Activity
etvedte commentedon Jun 4, 2026
Thanks, we were able to reproduce the issue. We'll look into this.
anthony-aylward commentedon Sep 22, 2026
Commenting to report that I encountered the same error when running the example
input_D_farinae_small.yamlwith-e singularityon nextflow version 26.04.6, and was also able to work around it by downgrading to nextflow version 25.04.3.murphyte commentedon Sep 22, 2026
yes, we are working on an update to support nextflow 26, but it probably won't be until EGAPx v1.0.2. In the meantime, please use 25.04.3