fix: canonical transcript mapped read extraction #561

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Run time

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Job	Run time
formatting	2m 2s
formatting	2m 2s
formatting	2m 2s
linting	49s
linting	49s
linting	49s
run-3prime-rna-workflow	51m 29s
run-3prime-rna-workflow	33m 17s
run-3prime-rna-workflow	40m 47s
run-rna-workflow	51m 10s
run-rna-workflow	51m 10s
run-rna-workflow	51m 10s
	4h 47m 36s