advisory for nf-core/ampliseq is missing incompatible Nextflow version

[FranBonath]

Describe the bug
nf-core/ampliseq does not run with Nextflow version 25.10.2 and produces a /bin/bash: line 10: .command.run: Permission denied error. There is an advisory on the website that describes this issue, but it limits the problem to Nextflow versions 25.04.0-25.04.3.

Error message

 Workflow execution completed unsuccessfully

The exit status of the task that caused the workflow execution to fail was: 126

Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY` terminated with an error exit status (126)


Command executed:

  taxref_reformat_standard.sh \
  
  #Giving out information
  echo -e "--dada_ref_taxonomy: silva=138\n" >ref_taxonomy.silva_138.txt
  echo -e "Title: Silva 138.1 prokaryotic SSU\n" >>ref_taxonomy.silva_138.txt
  echo -e "Citation: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28. PMID: 23193283; PMCID: PMC3531112.\n" >>ref_taxonomy.silva_138.txt
  echo "All entries: [title:Silva 138.1 prokaryotic SSU, file:[/proj/ngi2016003/nobackup/chuan/running_version/ampliseq-DB/silva_nr99_v138.1_train_set.fa.gz, /proj/ngi2016003/nobackup/chuan/running_version/ampliseq-DB/silva_species_assignment_v138.1.fa.gz], citation:Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28. PMID: 23193283; PMCID: PMC3531112., fmtscript:taxref_reformat_standard.sh, dbversion:SILVA v138.1 (https://zenodo.org/record/4587955)]" >>ref_taxonomy.silva_138.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_AMPLISEQ:AMPLISEQ:FORMAT_TAXONOMY":
      bash: $(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /vulpes/proj/ngis/ngi2016003/nobackup/NGI/ANALYSIS/P38402/ampliseq_analysis/work/3a/71a4d1d8be970b18a6faea96288dc8

Container:
  /vulpes/ngi/containers/biocontainers/containers.biocontainers.pro-s3-SingImgsRepo-biocontainers-v1.2.0_cv1-biocontainers_v1.2.0_cv1.img.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

[FranBonath]

not sure what to do with this info, or if this is even the correct interpretation. Would be nice for the person that discovered the issue to check if my error is reproducing what is described in the advisory.

[maxulysse]

I think we should update advisories to reflect this