Update focal-cn-preparation to use consensus SEG file in data download

[jaclyn-taroni]

The focal-cn-preparation module was taking over an hour to run in CI. This is because it was using the consensus SEG file that is committed to the repository, which is not for a subset of samples but instead contains all samples. With the release of v20, there's no reason to continue to use the file in analyses/copy_number_consensus_call/results so here I am changing the path in the second notebook of focal-cn-preparation to use the file in the data download. In the context of CI, this will be the subset file.

Closes #1129.

[jaclyn-taroni]

@jharenza and @kgaonkar6 - is there any reason (that you are aware of) that prohibits me from making this change at this point?

[jharenza]

I do not think so - the latest file is in the download.

[jaclyn-taroni]

We probably need to wait until all the v20 CNV changes go through though? Or would just getting #1123 through -> updating the release (if not done yet) be sufficient?

[kgaonkar6]

I've updated v20 release data with the latest consensus seg with #1123 b9284650be04df3538e6c6dba29b8eb0 pbta-cnv-consensus.seg.gz

I added the relative path so that we can run the code while running all the preprocessing steps of subtyping, so maybe we can add a logic to change to relative path or not within the if (params$base_run ==0)

OpenPBTA-analysis/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd

Lines 48 to 58 in a6281c2

	```{r}
	# TODO: the consensus SEG file is not currently in the data download -- when it
	# gets included we will have to change the file path here
	consensus_seg_file <- file.path("..", "copy_number_consensus_call", "results",
	"pbta-cnv-consensus.seg.gz")
	if ( params$base_run ==0 ){
	histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv")
	} else {
	histologies_file <- file.path("..", "..", "data", "pbta-histologies-base.tsv")
	}

[jaclyn-taroni]

In which scenario would you use the file in analyses/copy_number_consensus_call/results? When you use pbta-histologies-base.tsv?

[kgaonkar6]

yes, we will rerun the consensus seg file module first so the latest consensus seg file can be used as input for the focal-cn module

[jaclyn-taroni]

I'm not going to update the HTML for this notebook, because I expect that will happen as part of getting #1124 through anyway.

[jaclyn-taroni]

It is curious, though, that the consensus CN steps happens right before this one and I would expect then that the file in results for that module would then be from the subset of samples. There might be something snakemake-y happening that I don't understand.

[jaclyn-taroni]

Closing in favor of #1124