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>
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:
And the error was:
Reverting to an earlier version of nextflow fixed the issue: