Update nfosi jhu dataset

public/nst_nfosi_ntap/README.md

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+## Notes
+
+The patient cohort is from [The Johns Hopkins NF1 Biospecimen Repository](https://www.synapse.org/Synapse:syn53140231), which is an active biobanking project with rolling releases. It is funded by the [Neurofibromatosis Therapeutic Acceleration Program (NTAP)](https://www.n-tap.org/), led by Christine Pratilas, M.D., and David Loeb, M.D., Ph.D., with contributions from Angela Hirbe, PhD., and additional collaboration, data processing and data management by [NF-OSI / Sage Bionetworks](https://help.nf.synapse.org/NFdocs/about). 
+
+Patient raw sequencing data are generated by the institutional cores and shared on the secure Synapse platform with access restrictions. Sage Bionetworks does additional processing through the funded initiative described here: https://help.nf.synapse.org/NFdocs/data-processing. The [nf-core/rnaseq](https://nf-co.re/rnaseq/) workflow is used for gene expression from bulk RNA-seq and [nf-co.re/sarek](https://nf-co.re/sarek/) is used for somatic variant calling from whole exome sequencing (also for germline variant calling, but this is not shared on cBioPortal and only available on Synapse with access restrictons). After variant calling, variant annotation is done with [vcf2maf](https://github.com/Sage-Bionetworks-Workflows/nf-vcf2maf).
+
+Sage Bionetworks then appropriately packages the processed gene expression and mutations data with approved clinical data for contribution to cBioPortal, also funded by NTAP. Full clinical data are not contributed due to IRB restrictions. Released patient samples are confirmed with Christine Pratilas through an internal process. Updates may be occasionally made. For questions about clinical data and collaboration, please use the most up-to-date PI contact instructions on the [project space](https://www.synapse.org/Synapse:syn53133024/).

public/nst_nfosi_ntap/case_lists/cases_all.txt

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 cancer_study_identifier: nst_nfosi_ntap
 stable_id: nst_nfosi_ntap_all
 case_list_name: All samples
-case_list_description: All samples (19 samples)
+case_list_description: All samples (134 samples)
 case_list_category: all_cases_in_study
-case_list_ids: 2-010_Neurofibroma	2-026_Neurofibroma	2-013_Plexiform_Neurofibroma	2-004_Plexiform_Neurofibroma	2-012_Neurofibroma	2-031_Cell_Line	2-017_Neurofibroma	2-021_Neurofibroma	2-019_Neurofibroma	2-029_Neurofibroma	2-023_Plexiform_Neurofibroma	2-014_Neurofibroma	2-001_Plexiform_Neurofibroma	2-006_Plexiform_Neurofibroma	2-032_Plexiform_Neurofibroma	2-015_Plexiform_Neurofibroma	2-031_Malignant_Peripheral_Nerve_Sheath_Tumor	2-016_Neurofibroma	2-015_Neurofibroma
+case_list_ids: JH-2-075-3HE68-A	JH-2-082-G8357-A	JH-2-007-B14BB-AG2A6	JH-2-054-241HF-A	JH-2-002-GAF53-A1011	JH-2-085-F2983-F783D	JH-2-068-2BHHG-5F9FC	JH-2-111-G645D-6C5FF	JH-2-009-518B9-A	JH-2-016-6H516-A	JH-2-010-H915D-A	JH-2-017-9FH8F-A	JH-2-077-4H749-8GCFH	JH-2-014-AH466-96B78	JH-2-055-9F5F3-6G883	JH-2-068-A733G-A	JH-2-023-91HBD-A	JH-2-001-8A1B1-7B15A	JH-2-093-518GA-A	JH-2-100-19H33-94G2C	JH-2-003-H3G1H-HC8GG	JH-2-091-CAA8H-A	JH-2-021-6GFE7-A	JH-2-068-FH52C-A	JH-2-009-2578C-A	JH-2-079-CB92G-A	JH-2-021-6GFE7-7HBG6	JH-2-002-94FAA-A	JH-2-001-8A1B1-A	JH-2-095-4H3FE-A	JH-2-060-4CE8D-A	JH-2-076-41G1H-A	JH-2-079-9D31F-A	JH-2-006-D6BA4-BAEBD	JH-2-092-B52E5-A	JH-2-045-GH3AA-A	JH-2-045-F7H3C-A	JH-2-032-AE88A-A	JH-2-031-9GEA9-A	JH-2-055-1419H-9GG15	JH-2-002-GAF53-FB9H7	JH-2-029-7AE7F-GC2A3	JH-2-002-GAF53-A71AA	JH-2-012-HE58H-A	JH-2-013-7886G-A	JH-2-017-9FH8F-93DE8	JH-2-029-7AE7F-A	JH-2-032-AE88A-G36A1	JH-2-094-5HA24-A	JH-2-016-4H597-A	JH-2-045-GH3AA-D2C35	JH-2-103-H731E-A	JH-2-094-151G9-A	JH-2-044-83F15-A	JH-2-060-9G31E-HD38A	JH-2-002-94FAA-19DGB	JH-2-015-55B8D-2B9EB	JH-2-096-5E593-A	JH-2-091-CAA8H-GDFG1	JH-2-075-4F211-A	JH-2-055-FC9GH-A	JH-2-090-19D3F-A	JH-2-068-A7488-A	JH-2-089-H8EBA-HH51C	JH-2-002-FF824-A	JH-2-092-B4F11-A	JH-2-074-HE12C-A	JH-2-072-3DD4G-A	JH-2-009-518B9-77BH3	JH-2-100-19H33-A	JH-2-082-B5148-A92CA	JH-2-002-GAF53-2E57B	JH-2-023-1G2BC-A	JH-2-015-C436G-A	JH-2-016-4H597-15C1D	JH-2-019-DB5EH-A	JH-2-057-37D5D-A	JH-2-060-19EC4-A	JH-2-004-9D9D7-7EC36	JH-2-023-91HBD-2G2E2	JH-2-104-51E2H-A	JH-2-093-214AE-A	JH-2-019-DB5EH-C461C	JH-2-023-876HC-A	JH-2-085-F2983-A	JH-2-092-B4F11-2H1C1	JH-2-031-9GEA9-78GAB	JH-2-086-5EA11-A	JH-2-055-E1381-A	JH-2-002-FF824-C5E25	JH-2-054-9255F-A	JH-2-089-H8EBA-A	JH-2-099-26HCE-A	JH-2-002-354A1-A	JH-2-023-876HC-622H1	JH-2-104-51E2H-1G93A	JH-2-013-7886G-AA816	JH-2-094-5HA24-CC3H4	JH-2-060-99B2D-GG71G	JH-2-044-83F15-GA258	JH-2-015-G41AC-A	JH-2-086-5EA11-494GE	JH-2-023-89E1F-A	JH-2-016-6H516-818HB	JH-2-111-G645D-A	JH-2-010-H915D-BB99B	JH-2-076-41G1H-7FGE5	JH-2-026-9FD64-A	JH-2-093-214AE-H5A8H	JH-2-002-GAF53-3BAGC	JH-2-082-G8357-EG55A	JH-2-015-6AD96-A	JH-2-031-BFF3F-DG6C8	JH-2-014-AH466-A	JH-2-076-811H2-A	JH-2-015-55B8D-A	JH-2-068-2BHHG-A	JH-2-061-1H66H-AB35D	JH-2-090-19D3F-G36F6	JH-2-012-HE58H-37B26	JH-2-026-9FD64-HF616	JH-2-082-B5148-A	JH-2-006-D6BA4-A	JH-2-107-AGD39-1CH62	JH-2-075-3HE68-C61FE	JH-2-023-9DA42-A	JH-2-092-B52E5-BFCBA	JH-2-004-9D9D7-A	JH-2-090-59DE8-A	JH-2-077-88G11-A	JH-2-113-7857D-A	JH-2-102-3B72A-A	JH-2-023-1G2BC-82G48	JH-2-061-1H66H-A

public/nst_nfosi_ntap/case_lists/cases_sequenced.txt

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 cancer_study_identifier: nst_nfosi_ntap
 stable_id: nst_nfosi_ntap_sequenced
 case_list_name: Samples with mutation data
-case_list_description: Samples with mutation data (19 samples)
+case_list_description: Samples with mutation data (80 samples)
 case_list_category: all_cases_with_mutation_data
-case_list_ids: 2-010_Neurofibroma	2-026_Neurofibroma	2-013_Plexiform_Neurofibroma	2-014_Neurofibroma	2-001_Plexiform_Neurofibroma	2-006_Plexiform_Neurofibroma	2-004_Plexiform_Neurofibroma	2-032_Plexiform_Neurofibroma	2-015_Plexiform_Neurofibroma	2-016_Neurofibroma	2-012_Neurofibroma	2-031_Malignant_Peripheral_Nerve_Sheath_Tumor	2-031_Cell_Line	2-017_Neurofibroma	2-015_Neurofibroma	2-021_Neurofibroma	2-019_Neurofibroma	2-029_Neurofibroma	2-023_Plexiform_Neurofibroma
+case_list_ids: JH-2-100-19H33-A	JH-2-075-3HE68-A	JH-2-082-G8357-A	JH-2-113-7857D-A	JH-2-015-C436G-A	JH-2-054-241HF-A	JH-2-002-GAF53-A1011	JH-2-001-8A1B1-A	JH-2-009-2578C-A	JH-2-057-37D5D-A	JH-2-060-19EC4-A	JH-2-016-6H516-A	JH-2-023-1G2BC-A	JH-2-017-9FH8F-A	JH-2-068-A733G-A	JH-2-023-91HBD-A	JH-2-093-214AE-A	JH-2-103-H731E-A	JH-2-023-876HC-A	JH-2-085-F2983-A	JH-2-093-518GA-A	JH-2-086-5EA11-A	JH-2-055-E1381-A	JH-2-054-9255F-A	JH-2-089-H8EBA-A	JH-2-021-6GFE7-A	JH-2-068-FH52C-A	JH-2-002-354A1-A	JH-2-079-CB92G-A	JH-2-009-518B9-A	JH-2-002-94FAA-A	JH-2-045-F7H3C-A	JH-2-095-4H3FE-A	JH-2-060-4CE8D-A	JH-2-076-41G1H-A	JH-2-079-9D31F-A	JH-2-092-B52E5-A	JH-2-045-GH3AA-A	JH-2-074-HE12C-A	JH-2-032-AE88A-A	JH-2-031-9GEA9-A	JH-2-023-89E1F-A	JH-2-055-1419H-9GG15	JH-2-099-26HCE-A	JH-2-002-GAF53-FB9H7	JH-2-111-G645D-A	JH-2-012-HE58H-A	JH-2-013-7886G-A	JH-2-026-9FD64-A	JH-2-029-7AE7F-A	JH-2-015-6AD96-A	JH-2-094-5HA24-A	JH-2-016-4H597-A	JH-2-014-AH466-A	JH-2-076-811H2-A	JH-2-015-55B8D-A	JH-2-010-H915D-A	JH-2-094-151G9-A	JH-2-044-83F15-A	JH-2-096-5E593-A	JH-2-006-D6BA4-A	JH-2-104-51E2H-A	JH-2-019-DB5EH-A	JH-2-023-9DA42-A	JH-2-075-4F211-A	JH-2-082-B5148-A	JH-2-055-FC9GH-A	JH-2-090-19D3F-A	JH-2-004-9D9D7-A	JH-2-090-59DE8-A	JH-2-077-88G11-A	JH-2-015-G41AC-A	JH-2-102-3B72A-A	JH-2-002-FF824-A	JH-2-092-B4F11-A	JH-2-068-A7488-A	JH-2-068-2BHHG-A	JH-2-091-CAA8H-A	JH-2-072-3DD4G-A	JH-2-061-1H66H-A

public/nst_nfosi_ntap/meta_mrnaseq_tpm.txt

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+cancer_study_identifier: nst_nfosi_ntap
+genetic_alteration_type: MRNA_EXPRESSION
+datatype: CONTINUOUS
+stable_id: mrna_seq_tpm
+show_profile_in_analysis_tab: true
+profile_name: Normalized gene expression
+profile_description: Normalized gene expression levels (TPM)
+data_filename: data_mrnaseq_tpm.txt