Updated analysis: Add README files to any analysis without a README

[sjspielman]

What analysis module should be updated and why?

The following analysis modules are missing README.md documentation files:

• copy_number_consensus_call/
• sex-prediction-from-RNASeq/
• comparative-RNASeq-analysis/
• focal-cn-file-preparation/
• sv-analysis/
• ssgsea-hallmark/
• survival-analysis/
• fusion_filtering/
• selection-strategy-comparison/

Why should the module be updated?

Modules should contain clear documentation about specific goals, input, output, and pipelines to ensure reproducibility and to facilitate use by other contributors.

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

For all completed modules, README.md files should explain:

• The source (authorship) of the analysis
• The purpose of the analysis
• The analysis pipeline, if multiple scripts are run for the analysis
• The output/outcome of the analysis

For all in progress modules, README.md files should explain, at a minimum, analysis goals and expected output/outcomes.

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

N/A

When do you expect the revised analysis will be completed?

Pending availability of module authors, as long as completed before publication. This is not strictly urgent, unless these analyses are specifically required for future analyses and added documentation will strongly facilitate.

Who will complete the updated analysis?

I have compiled, for each directory missing a README, who I believe the authors are, based either on PRs or code comments. In each case it may be more appropriate for others who handled the associated PR (such as @jaclyn-taroni , @jharenza , @jashapiro , @cgreene , etc) to assist in compiling these details:

• copy_number_consensus_call/ : @fingerfen
• sex-prediction-from-RNASeq/: @bill-amadio
• comparative-RNASeq-analysis/: @GeoffLyle
• focal-cn-file-preparation/: @jaclyn-taroni
• sv-analysis/: @yangyangclover
• ssgsea-hallmark/: @PichaiRaman (although some comments in code indicate maybe @cbethell?)
• survival-analysis/: @cansavvy
• fusion_filtering/: @kgaonkar6
• selection-strategy-comparison/: @jashapiro

[jaclyn-taroni]

A few notes on a few of the more mature modules:

• Some of these are tracked individually: #319 #320
• ssgsea-hallmark should get addressed at the same time as #235 in my opinion
• I'm on selection-strategy-comparison this morning as part of #360

[jaclyn-taroni]

Oh, also consistent the change in #346 making these a requirement!

[bill-amadio]

I am working to complete the README and fourth (final) script of the sex-prediction-from-RNASeq pipeline by January 7.

[kgaonkar6]

added README for fusion_filtering