Rerun TMB calculation - test run

[AntoniaChroni]

Purpose/implementation Section

What scientific question is your analysis addressing?

This is a test run for re-running the TMB-calculation module.

The following will need to be addressed later on:

1. The biospecimen_id_to_bed_map.tsv file was transferred from the data_dir and we renamed any misspelled files related to the ashion_exome....bed files.
2. Shell and R script files call the input file from input_dir. This must be updated to data_dir when files are named properly in the data/biospecimen_id_to_bed_map.tsv file, and re-run the module.

What was your approach?

What GitHub issue does your pull request address?

This is related to ticket #430 (comment)

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

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

Results

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

The following files are updated in the results_dir:

1. snv-mutation-tmb-all.tsv and
2. snv-mutation-tmb-coding.tsv

What is your summary of the results?

• snv-mutation-tmb-all.tsv contains 4150 records (compared to 2766 in the previous file).
• snv-mutation-tmb-coding.tsv contains 4146 records (compared to 2764 in the previous file).

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.

[jharenza]

Reran and everything is the same, thank you for putting this in so quickly!

[jharenza]

closes #430