Hello! I am currently reviewing pipelines that are missing their AWS full size test results. Looks like genomeassembler has some parameter validation errors, if someone could look into it:

ERROR ~ Cannot invoke method toBoolean() on null object
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/prepare_shortreads/main.nf' at line: 37 or see 'nf-3Raqkm5qxoyOec.log' file for more details
ERROR ~ Argument of `file()` function cannot be null
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf' at line: 76 or see 'nf-3Raqkm5qxoyOec.log' file for more details
ERROR ~ Argument of `file()` function cannot be null
-- Check script '.nextflow/assets/nf-core/genomeassembler/subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf' at line: 81 or see 'nf-3Raqkm5qxoyOec.log' file for more details
-[nf-core/genomeassembler] Pipeline completed with errors-
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
-- Check 'nf-3Raqkm5qxoyOec.log' file for details

Platform link: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3Raqkm5qxoyOec/v2/logs let me know if you don't have the necessary access

Yup, this is currently broken because I refactored the pipeline, and updated the test-samplesheet for the new version, which is incompatible with the old version

any chance to keep the old samplesheet and move the new samplesheet to a new subdirectory orgive it a new name? See sarek for example: https://github.com/nf-core/test-datasets/tree/sarek/testdata/tsv tsv is purely kept around for versions >3.0.0 and older

Ok I have restored the previous samplesheet and made a different one for the new version

thanks I resubmitted the run 🤞

I'm getting stuck with Flye assembly, with Flye being passed a "-1" g as genome size, is it possible to set a default if genomescope cannot make an estimate?

Command error:
  [2026-02-19 15:19:38] INFO: Starting Flye 2.9.5-b1801
  Traceback (most recent call last):
    File "/opt/conda/bin/flye", line 11, in <module>
      sys.exit(main())
               ^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/flye/main.py", line 761, in main
      _run(args)
    File "/opt/conda/lib/python3.12/site-packages/flye/main.py", line 455, in _run
      _set_genome_size(args)
    File "/opt/conda/lib/python3.12/site-packages/flye/main.py", line 409, in _set_genome_size
      args.genome_size = human2bytes(args.genome_size.upper())
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/flye/utils/bytes2human.py", line 104, in human2bytes
      num = float(num)
            ^^^^^^^^^^
  ValueError: could not convert string to float: ' '

https://nf-co.re/genomeassembler/dev/parameters/#genome_size i think

Will that parameter then be used in all samples or only when genomescope doesn't work?

No, it will then be used in all samples