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end-to-end test the new features
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- tabmut: --add-mutations
- coocmutbamscan: --fix-subsets
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DrYak committed Nov 27, 2024
1 parent 26dc7a5 commit 5c35542
Showing 1 changed file with 23 additions and 1 deletion.
24 changes: 23 additions & 1 deletion tests/test_integration.py
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,19 @@ def test_workflow():
"amplicons.v3.yaml",
]
)
subprocess.check_call(
[
"cojac",
"cooc-mutbamscan",
"-b",
"nCoV-2019.insert.V3.bed",
"-m",
"voc/",
"--fs",
"-A",
"amplicons.v3.fixedsub.yaml",
]
)
subprocess.check_call(
[
"cojac",
Expand Down Expand Up @@ -141,7 +154,16 @@ def test_workflow():
]
)
subprocess.check_call(
["cojac", "cooc-tabmut", "-j", "cooc-test.json", "-o", "cooc-export.csv"]
[
"cojac",
"cooc-tabmut",
"-j",
"cooc-test.json",
"--am",
"amplicons.v3.yaml",
"-o",
"cooc-export.csv",
]
)

# primers affected by mutations
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