Move gene_match module and modify

[runjin326]

What analysis module should be updated and why?

https://github.com/d3b-center/D3b-codes/tree/master/gene_match

1. Move this gene match module to PediatricOpenTargets
2. Change the file paths to directly take files from the data in the QC code
3. Filter the output ensg-hugo-pmtl-mapping.tsv as described below

What changes need to be made? Please provide enough detail for another participant to make the update.

Currently this file has this line:

ensg_id gene_symbol            pmtl      version
Symbol_Not_Found     NA Relevant Molecular Target PMTL version 1.1

Please modify the code that generated this file to filter any line that has ensg_id == "Symbol_Not_Found &gene_symbol` == NA

What input data should be used? Which data were used in the version being updated?

v10
snv-consensus-plus-hotspots.maf.tsv.gz
consensus_wgs_plus_cnvkit_wxs.tsv.gz
gene-expression-rsem-tpm-collapsed.rds
fusion-putative-oncogenic.tsv
and input files from the module

When do you expect the revised analysis will be completed?

1 day

Who will complete the updated analysis?

[sangeetashukla]

@runjin326 I will start working on this.

[jharenza]

closing with #145