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Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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Parsing of nextflow.config crash #3

Closed aghozlane closed 1 year ago

aghozlane commented 1 year ago

Hello,

I can't use the conda install, but I guess I do have all dependencies already installed. I am trying to use the profile singularity_slurm, but the demo crash when parsing nextflow.config with the following error:

$../nextflow run main_AMR++.nf -profile singularity_slurm --pipeline demo
Unable to parse config file: '/***/***/***/aghozlan/AMRplusplus/nextflow.config'

  Compile failed for sources FixedSetSources[name='/groovy/script/ScriptC7B9CD1F2358AA28CEFA0230C7243C79']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/ScriptC7B9CD1F2358AA28CEFA0230C7243C79: 16: Unexpected input: '{' @ line 16, column 9.
     process {

I tried nextflow version 22.10.2.5832, nextflow version 20.10.0.5430. We have apptainer 1.0.3 instead of singularity.

Any idea ?

EorgeKit commented 1 year ago

Issue #4

EnriqueDoster commented 1 year ago

Hello @aghozlane , could you please try running this again using the most recent AMR++ code and let us know how it goes? I believe we fixed the issue with the nextflow.config file, but server settings can sometimes make working with singularity and slurm difficult.

EnriqueDoster commented 1 year ago

We are closing this issue as the latest updates to AMR++ v3.0.1 should address this error. Please let us know if you run into any further issues. Thank you!