Move gene match

[sangeetashukla]

Purpose/implementation Section

Move gene_match module from D3B-codes to OpenPedCan for downstream updates/analysis

What was your approach?

Copy files over from D3B-codes/gene_match

What GitHub issue does your pull request address?

Issue 231

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Please review if all files were successfully moved over here

Is there anything that you want to discuss further?

The next steps of the linked issue will be completed in a separate PR

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

NA

What types of results are included (e.g., table, figure)?

qc_ensg_hugo_pmtl_mapping.nb.html
merge_gencode_v28_v38_open_ped_can_v7_gene_ensg_symbol_mapping_files.R
add_pmtl_ens_hugo.Rmd
run-gene-mapping.sh
README.md
gene_ensembl_id_from_gtf.R
add_pmtl_ens_hugo.nb.html
qc_ensg_hugo_pmtl_mapping.Rmd
input/gencode.v28.annotation.gtf.gz
input/RMTL_v1.0.tsv
input/open_ped_can_v7_ensg-hugo-rmtl-mapping.tsv
input/PMTL_v1.1.tsv
input/gencode.v38.annotation.gtf.gz
results/ensembl_gene_symbol_gtf_genode_v28_v38_open_ped_can_v7_merged.tsv
results/ensg-hugo-pmtl-mapping.tsv
results/ensembl_gene_symbol_gtf_genode_v28.tsv
results/ensembl_gene_symbol_gtf_genode_v38.tsv

What is your summary of the results?

NA

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[runjin326]

I am very confuse right now :

Why does this PR still have so many commits?

[sangeetashukla]

Hi, I think I know what happened.
I had merged my local branch to dev earlier for the PMTL updates, before we received information about the existing D3B-codes/gene_match module. And then, since we started working on the gene_match module, my PR was not merged.
Having said that, I must have missed deleting the directory (unwanted one) from my dev, and pushing that change.
Would you mind moving the gene_match files over so my commits merged while I fix my dev?
And then I will make the rest of the updates in the directory, in a new local branch.
Sorry about the confusion.

[runjin326]

@sangeetashukla, ya I was thinking about this and I just wanted to mention that we do not want to make any commit to our dev - that needs to be in sync with the upstream dev. We only make commits to any branch that we are working on and we sync our branch to our local dev (which is in sync with the upstream dev).
There are two ways of solving this:

1. Rebase your dev to what upstream dev
2. If you don't have any active branch that you are working on - delete the repo, git clone the repo, set upstream and work from there (that way you would have a clean base)