Rerun all of the modules with the new docker image

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rerun all of the modules with the new docker image.

What was your approach?

• Rerun the entire module and update any module that fails or has warnings as a result of deprecated R or Python functions as a result of newer packages/modules
• Update Dockerfile if any dependency is missing

What GitHub issue does your pull request address?

• Rerun all of the modules with the new docker image ticket-tracker-OPC#556

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

Which areas should receive a particularly close look?

Provide suggestions if any other module apart from those listed below Utilized in OPC need to be included and checked for updates:
[Dockerfile]

• install ubuntu libncurses5 library required for GISTIC runs

[Rerun data pre-release analysis modules]

• independent-samples
• fusion_filtering
• run-gistic
• focal-cn-file-preparation
• fusion-summary
• tmb-calculation
• tp53_nf1_score
• data-pre-release-qc

[Rerun molecular subtyping and addition data pre-release module]

• molecular-subtyping-ATRT
• molecular-subtyping-chordoma
• molecular-subtyping-CRANIO
• molecular-subtyping-embryonal
• molecular-subtyping-EPN
• molecular-subtyping-EWS
• molecular-subtyping-HGG
• molecular-subtyping-LGAT
• molecular-subtyping-MB
• molecular-subtyping-neurocytoma
• molecular-subtyping-pathology
• molecular-subtyping-integrate
• independent-samples
• create-subset-files

[Rerun data post-release modules]

• gene_match
• efo-mondo-mapping
• mtp-annotations
• long-format-table-utils
• fusion-frequencies
• cnv-frequencies
• snv-frequencies
• rna-seq-expression-summary-stats
• filter-mtp-tables
• mtp-tables-qc-checks
• rnaseq-batch-correct

Is there anything that you want to discuss further?

NA

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

YES

Results

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

Module results that can be uploaded to GitHub with PR

What is your summary of the results?

Successful module runs with new docker image

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]

@ewafula is this done/complete? Also noticed cnv consensus wasn't in here, was that bc of the known issue or just forgotten - in any case, you did test it, so yay!

[ewafula]

Yes, this one is done. I intentionally left our the cnv consensus module because I was focused on debugging the the snakemake workflow. Turns out it was docker issue associated Debian Stretch limitations. Can be merged.

I also left out the cnv consensus module from the repo README update for the data release process because you had suggested that it needs to wrapped in CWL and run on CAVATICA with as pre-release workflows.

[jharenza]

Ok thanks- can you put into the release readme for now then since fixed

[jharenza]

I think the TP53 changes are happening because we don't have a seed set for this, and we should, though it does not affect the overall call for these samples. I will create a ticket for this.