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- use synonymous mutation rates instead of relative mutrates - use mutation rate for omegagloballoc and mutated reads rate for omegamultigloballoc - add all_samples mutational profile to omega input - rename scripts and modules accordingly to the changes
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This was referenced Dec 21, 2024
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FerriolCalvet
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FerriolCalvet
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Dec 21, 2024
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all good!
let's merge it, and if after we revise omega code we see that there is any change required we'll fix that
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After fixing the filtering of mutations and realizing that the redistribution of the numbers of synonymous mutations per gene per sample could be improved by using the depth per position but also the mutational profile of the sample and the full cohort, we had to make some changes in the omega modules and subworkflow.
In addition to the changes described above, we are also updating the container name for the omega modules to reflect an updated version, we should formalize this as soon as we start defining a version naming for omega.
I DO NOT EXPECT ANY ADDITIONAL CHANGES IN deepCSA (this is the reason for opening the PR)
BUT DO NOT MERGE UNTIL ALL THIS IS CHECKED, SINCE WE MIGHT NEED CHANGES IN the omega version/implementations