need to update samples fillout workflow output

[stevekm]

• need to update all portal files to include data for all new DMP samples included in output
• need to output "shareable" maf (current output), and "portal" output that has comments removed
• need to generate data mutations uncalled output (Make data_mutations_uncalled and meta_mutations_uncalled files for cBioPortal #63)

@timosong @svural

[timosong]

need to generate data mutations uncalled output (#63)
Current output should be 4 maf files:

1. "unfiltered" maf. Has no filters that have distinction between clinical and research samples. This should end up in analysis folder
2. "filtered" maf. Germline filters, has distinction between clinical and research. This should end up in analysis folder
3. data_mutations_extended.txt. This file has fewer columns than file 2 filtered. This should end up in portal folder
4. data_mutations_uncalled.txt. This file has fewer columns than file 2 filtered. This should end up in portal folder

Number of rows of file#3 and file#4 equal number of rows in file 2.

need to update all portal files to include data for all new DMP samples included in output.

The following files need to be updated.

1. data_mutations_extended.txt. Need to find out what columns can be filled from DMP data and what can be left blank. The only necessary columns are GENE_PANEL, PATIENT_ID, SAMPLE_ID.
2. case_lists files need to have new DMP ids appended. (tab delimited at end of case_list_ids)
   case_lists/cases_all.txt
   case_lists/cases_cnaseq.txt
   case_lists/cases_cna.txt
   case_lists/cases_sequenced.txt

new files need to be created:

1. meta_mutations_uncalled.txt
   cancer_study_identifier: pilot_msk_melpcm
   data_filename: data_mutations_extended.txt
   datatype: MAF
   genetic_alteration_type: MUTATION_EXTENDED
   profile_description: Mutation data
   profile_name: Mutations
   show_profile_in_analysis_tab: true
   stable_id: mutations
   namespaces: ASCN

Caveats.
Nice to have is DMP Copy number merged in if fillout was ever performed.
This also means that there may be DMP ids present in copy number, but not in fillout and vice versa. So we need to create a union of all dmp ids and then add that to the above files (case_lists, data_clinical_sample)

[stevekm]

@timosong I think the "uncalled" mutations files should be a separate issue, are they required for fillout data import?

[stevekm]

• case list files should not contain duplicate sample ID's
• the data mutations uncalled file is required for fillout delivery to cBioPortal
• the fillout output .maf mutation data should be merged into the data_mutations_extended.txt which is currently generated by the portal-workflow.cwl for cBioPortal import

[stevekm]

case list fixes are implemented