Set pipefail for Cram tests #2872

Job	Run time
pathogen-repo-ci (dengue)	2m 37s
pathogen-repo-ci (lassa)	53s
pathogen-repo-ci (measles)	1m 19s
pathogen-repo-ci (mpox)	1m 11s
check-docs	35s
mypy	52s
pathogen-repo-ci (seasonal-cov)	1m 47s
pathogen-repo-ci-v0 (avian-flu)	51s
pathogen-repo-ci (zika)	1m 3s
pathogen-repo-ci-v0 (ebola)	1m 0s
pathogen-repo-ci-v0 (mumps)	52s
pyright	14s
test (python=3.8 biopython=1.80)	11m 29s
pathogen-repo-ci-v0 (ncov)	55s
test (python=3.8 biopython=latest)	11m 55s
pathogen-repo-ci-v0 (rsv)	8m 26s
test (python=3.9 biopython=1.80)	11m 55s
pathogen-repo-ci-v0 (seasonal-flu)	1m 7s
test (python=3.9 biopython=latest)	12m 17s
pathogen-repo-ci-v0 (tb)	1m 13s
test (python=3.10 biopython=1.80)	12m 28s
test (python=3.10 biopython=latest)	12m 17s
test (python=3.11 biopython=1.80)	11m 58s
test (python=3.11 biopython=latest)	12m 20s
build-docs / build-conda	0s
build-docs / build-pip	2m 6s
codecov	16s
	2h 3m 56s

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