Migrate CI workflow from apt-get to conda/miniforge

[Copilot]

The CI workflow was using apt-get to install dependencies, which provided limited versions and missing packages. This migrates to conda/miniforge for better bioinformatics tooling support.

Changes

• Setup conda environment: Added conda-incubator/setup-miniconda@v3 with miniforge, using conda-forge and bioconda channels with strict priority
• Install all dependencies via conda: Replaced apt-get with conda install for samtools, bcftools, freebayes, bedtools, bwa, minimap2, parallel, vcflib, vt, snpeff, seqtk, snp-sites, wgsim, any2fasta, perl-bioperl, and samclip
• Shell configuration: Added shell: bash -el {0} to all steps to ensure conda environment activation

- name: Setup Miniforge
  uses: conda-incubator/setup-miniconda@v3
  with:
    miniforge-version: latest
    activate-environment: snippy-env
    channels: conda-forge,bioconda
    channel-priority: strict

- name: Install Dependencies
  shell: bash -el {0}
  run: |
    conda install -y \
      samtools bcftools freebayes bedtools \
      bwa minimap2 parallel vcflib vt snpeff \
      seqtk snp-sites wgsim any2fasta \
      perl-bioperl samclip

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Create a CI workflow using conda</issue_title>
<issue_description>Please fix the CI workflow
It should enable conda and miniforge
And install samtools, bcftools, freebayes, etc
</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Create a CI workflow using conda #623

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