Updated analysis: copy_number_consensus_call_manta to use only samples which do not have GATK CNV

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

What was your approach?

Create a script/update a script to pull in only WGS samples which are not present in the cnv-gatk.seg.gz file and run the consensus using manta SV instead.

What GitHub issue does your pull request address?

#387

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

Which areas should receive a particularly close look?

script/missing_WGS.R
run_consensus_call.sh

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)?

table

What is your summary of the results?

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]

@zzgeng can you update the name of this output file to read cnv-consensus-manta.seg.gz and cnv-consensus-manta.tsv

[jharenza]

I forgot this requires an update to CI testing files to enrich for these non-GATK samples in order to pass. Will create a ticket.

[jharenza]

All modules, including this one passed CI 👍