Set pipefail for Cram tests #2899

Job	Run time
mypy	49s
pathogen-repo-ci (dengue)	2m 43s
check-docs	35s
pathogen-repo-ci (lassa)	52s
pathogen-repo-ci-v0 (avian-flu)	50s
pathogen-repo-ci (measles)	1m 22s
pathogen-repo-ci-v0 (ebola)	52s
pyright	22s
pathogen-repo-ci (mpox)	1m 23s
pathogen-repo-ci-v0 (mumps)	52s
pathogen-repo-ci (seasonal-cov)	2m 1s
test (python=3.8 biopython=1.80)	11m 40s
pathogen-repo-ci (zika)	1m 15s
test (python=3.8 biopython=latest)	11m 51s
pathogen-repo-ci-v0 (ncov)	1m 8s
test (python=3.9 biopython=1.80)	13m 30s
pathogen-repo-ci-v0 (rsv)	8m 45s
test (python=3.9 biopython=latest)	12m 57s
pathogen-repo-ci-v0 (seasonal-flu)	1m 22s
test (python=3.10 biopython=1.80)	12m 23s
pathogen-repo-ci-v0 (tb)	1m 14s
test (python=3.10 biopython=latest)	12m 26s
test (python=3.11 biopython=1.80)	12m 23s
test (python=3.11 biopython=latest)	12m 48s
build-docs / build-conda	0s
build-docs / build-pip	2m 24s
codecov	17s
release	0s
rebuild-docker-image	0s
	2h 9m 4s

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