renamed WTS input parameter mainly to get rid of pipeline (dragen/bcbio) specific names
renamed WGS input (umccrise) parameter for the same reason as above
dropped pizzly support. It has not been updated since 2016 and issues are also not updated.
The input folders still use names for three tools (arriba, salmon and purple). Perhaps, we can rename purple to CNV? This is related to umccrise outputs. Happy to take input on this.
The folder names for arriba and salmon are simpler to update as these can be tackled at WTS workflow level (that is, if we want to rename these as well).
Note:
The imp change wrt to our internal pipeline is moving quantification output to a folder named salmon. This can be tackled when we test the package on ICA.
Main updates:
The input folders still use names for three tools (
arriba,salmonandpurple). Perhaps, we can rename purple toCNV? This is related to umccrise outputs. Happy to take input on this.The folder names for
arribaandsalmonare simpler to update as these can be tackled at WTS workflow level (that is, if we want to rename these as well).Note:
The imp change wrt to our internal pipeline is moving quantification output to a folder named
salmon. This can be tackled when we test the package on ICA.