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Ran 02 May 2026 02:12AM UTC

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Committed 08 Apr 2026 08:46AM UTC coverage: 80.723%. Remained the same

Job # 25241009594.1

Build Type

push

github

Committed by

cokelaer

Commit Message

Simplify variant_calling apptainer workflow to match local working setup

- Remove image cache (was potentially causing issues)
- Remove deprecated --use-apptainer flag
- Remove --annotation-file (not needed for variant_calling)
- Add --force and --monitor flags
- Simplify to just run sequana_variant_calling command (no bash script)
- Match the local command that works: sequana_variant_calling --input-directory
  test/data/ --force --monitor --reference-file test/data/JB409847.fasta
  --apptainer-prefix ~/.apptainer/cache

Coverage Stats

67 of 83 relevant lines covered (80.72%)

0.81 hits per line

cokelaer / variant_calling / 25241009594 / 1
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main: 81%

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cokelaer / variant_calling / 25241009594 / 1 81% main: 81%

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Source Files on job 25241009594.1

cokelaer / variant_calling / 25241009594 / 1
81%
main: 81%

README BADGES
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