D3b Bix Dev Feature: Fix bug

[migbro]

✨

[Required] Is this a new tool/workflow?

No

[Required] Which tools/workflows would you like to update/add?

Provide software links and dockerPull location if applicable

analyses/collapse-rnaseq/cwl/scripts/liftover_collapse_rnaseq.py

[Required] What features (new params, inputs, outputs, etc) would you like to add to each?

Add reference files and test input locations if applicable

return happens too soon, causing all duplicate genes to be collapsed to be dropped, except one, in

OpenPedCan-analysis/analyses/collapse-rnaseq/cwl/scripts/liftover_collapse_rnaseq.py

Lines 63 to 71 in a78b0e3

	def collapse_dups(dup_gene_sym_dict):
	"""
	Get highest mean for repeated gene symbols and output that row
	"""
	for gene_sym in dup_gene_sym_dict:
	means = [mean(data) for data in dup_gene_sym_dict[gene_sym]]
	top_idx = means.index(max(means))
	out_data = "{}\t{}\n".format(gene_sym, '\t'.join(list(map(str, dup_gene_sym_dict[gene_sym][top_idx]))))
	return out_data

[Optional] How long do you think this work will take?

an hour

[Optional] Who will complete this work?

@migbro

Ticket will be considered resolved either by a successful PR with updated release if applicable, or a simple denial of the request backed by a good reason

[jharenza]

completed with #553