error in running MpGAP with SRR8482585_30X_{1,2}.fastq.gz and SRX5299443_30X.fastq.gz

[CaiBiotech]

When I tried to test the complete workflow of your code, I found that the case file at https://figshare.com/ndownloader/articles/14036585/versions/4 can pass through the ngs-preprocess pipeline, but when I continue with the MpGAP pipeline, an error occurs. The code I tried is as follows: nextflow run fmalmeida/mpgap \ --output mpgap_assmbly \ --max_cpus 20 \ --genome_size 6m \ --input ./mpgap_samplesheet.yml \ --hybrid-strategy both \ -profile docker

running log .nextflow.log

[fmalmeida]

Hi @CaiBiotech , Thanks for using the pipeline and for sharing.

The error is super odd, specially comming from the dump sofwares, with such message:

Traceback (most recent call last):
    File ".command.sh", line 101, in <module>
      main()
    File ".command.sh", line 69, in main
      raise AssertionError(
  AssertionError: We assume that software versions are the same between all modules. If you see this error-message it means you discovered an edge-case and should open an issue in nf-core/tools.

Can you share the contents of the following directory so I can try to find the culprit? --> /share/home/dw_user0001/easy_genome/job20240429/work/67/de629a449b02e7d503777c6a1087bb.

I believe github allows you to share compressed files.

[fmalmeida]

That would be very helpful because, when trying to reproduce it, using the test case file you mentioned, which is the same one in the Quickstart section of the pipeline's online manual.

When using the commands from there to run it, it finished successfully:

nextflow run fmalmeida/mpgap \
  --output _ASSEMBLY \
  --max_cpus 5 \
  --skip_spades \
  --input "samplesheet.yml" \
  --unicycler_additional_parameters ' --mode conservative ' \
  -profile docker --hybrid_strategy both -r master -latest

So, having the directory mentioned would be helpful to try to understand what happened. But, meanwhile, I would suggest you try running again to check if it reproduces.

[CaiBiotech]

Updating Nextflow to version 23.10.1 seems to have resolved the issue. Thank you!

[fmalmeida]

Awesome! I should consider then increasing the “minimum version” required to avoid it in the future. Many thanks for reporting!