feat: add fermikit single-thread option

[jonasfreimuth]

This is a re-creation of TRON-Bioinformatics#1 for merging into the upstream.

This PR has been (largely) created using Copilot, but I have reviewed all changes and have run the example/test_all.sh script on this code.

Original text from copilot

The genotyping pipeline re-aligns reads against a de-novo HLA assembly, but fermikit assembly can vary across runs when multi-threaded. This change adds an explicit option to keep the overall pipeline threaded while forcing the fermikit assembly step itself to run single-threaded for reproducible contig construction.

• New CLI control

  • Adds -F to script/whole/SpecHLA.sh to force the fermikit de-novo assembly stage to run with one thread.
  • Mirrors the same option in script/whole/test_SpecHLA.sh to keep the test entrypoint aligned with the main CLI.

• Scoped threading change

  • Passes the new flag through to script/run.assembly.realign.sh.
  • Applies the override only to fermi2.pl unitig.
  • Leaves all other thread-aware commands in the re-alignment stage on the user-provided -j thread count.

• Documentation

  • Updates CLI help text and README.MD to expose the new option and intended behavior.

Example:

# Keep the pipeline at 8 threads, but force fermikit assembly to use 1
bash script/whole/SpecHLA.sh -n sample -1 sample.R1.fq.gz -2 sample.R2.fq.gz -j 8 -F

Original prompt

During genotyping, there is a re-alignment step to a de-novo assembly of the HLA regions. Plase add an option to force the fermikit de-novo assembly step to always run single-threaded regardless of the threads provided to the genotyping command. The intention is to ensure that this always runs reproducibly, as fermikit is known to be non-deterministic in constructing assemblies.

Created from VS Code.