ci: fix Apptainer install by dropping Launchpad PPA

[Copilot]

add-apt-repository ppa:apptainer/ppa intermittently times out on GitHub-hosted runners, causing flaky CI failures unrelated to test code.

Changes

• Install: Replace PPA-based install (software-properties-common → add-apt-repository → apt install) with a direct download of the latest .deb from the official Apptainer GitHub releases; add apptainer --version to confirm.
• Cache: Remove brittle caching of system paths (/usr/bin/apptainer, /usr/lib/apptainer, /etc/apptainer) and the unused APT archives cache. Retain only ~/.apptainer/cache, moved before the install step.
• Action version: Bump actions/cache@v3 → actions/cache@v4.

# Before
- name: Install Apptainer
  if: steps.cache-apptainer.outputs.cache-hit != 'true'
  run: |
    sudo apt-get install -y software-properties-common
    sudo add-apt-repository -y ppa:apptainer/ppa  # ← flaky
    sudo apt-get update && sudo apt-get install -y apptainer

# After
- name: Install Apptainer
  run: |
    APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
      | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
    wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
    sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
    apptainer --version

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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[coveralls]

Coverage Report for CI Build 25227416281

Coverage remained the same at 80.0%

Details

• Coverage remained the same as the base build.
• Patch coverage: No coverable lines changed in this PR.
• No coverage regressions found.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

No coverage regressions found.

---

Coverage Stats

Relevant Lines:	70
Covered Lines:	56
Line Coverage:	80.0%
Coverage Strength:	1.6 hits per line

---

💛 - Coveralls

[cokelaer]

@copilot check the original PR from sequana/fastqc. there was an update wrt apptainer installation

[Copilot]

@copilot check the original PR from sequana/fastqc. there was an update wrt apptainer installation

Updated in 2806c9c. The install now matches sequana/fastqc#41 exactly — downloading the latest .deb directly from GitHub releases rather than using Ubuntu's default apt repos:

- name: Install Apptainer
  run: |
    APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
      | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
    wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
    sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
    apptainer --version