New data: CMI/DGD tumor only, DGD T/N, Organoid RNA-Seq

[jharenza]

Which new datasets are being added with this release?

What is the sample breakdown (number of WGS, WXS, RNA-Seq, Panel, Methylation, other)?

https://d3b.atlassian.net/browse/BIXU-3767

What module(s) generated any new files to include in the release? Has that module been added to the analysis/README.md, and to CI?

Are you aware of any modules impacted by the file(s) change(s)? Describe if the file name is changed.

What data file(s) are added/updated/removed in this release?

[Pre-release files]

• [ ] histologies-base.tsv
• [ ] cnv-cnvkit.seg.gz
• [ ] cnvkit_with_status.tsv
• [ ] cnv-controlfreec.tsv.gz
• [ ] cnv-consensus-gistic.zip
• [ ] cnv-consensus.seg.gz
• [ ] consensus_seg_with_status.tsv
• [ ] consensus_wgs_plus_cnvkit_wxs.tsv.gz
• [ ] consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz
• [ ] consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz
• [ ] fusion-arriba.tsv.gz
• [ ] fusion-dgd.tsv.gz
• [ ] fusion-putative-oncogenic.tsv
• [ ] fusion-starfusion.tsv.gz
• [ ] fusion_summary_embryonal_foi.tsv
• [ ] fusion_summary_ependymoma_foi.tsv
• [ ] fusion_summary_ewings_foi.tsv
• [ ] fusion_summary_lgat_foi.tsv
• [ ] snv-consensus-plus-hotspots.maf.tsv.gz
• [ ] snv-dgd.maf.tsv.gz
• [ ] sv-manta.tsv.gz
• [ ] snv-mutation-tmb-all.tsv
• [ ] snv-mutation-tmb-coding.tsv
• [ ] gene-expression-rsem-tpm-collapsed.rds
• [ ] gene-counts-rsem-expected_count-collapsed.rds
• [ ] tcga-gene-expression-rsem-tpm-collapsed.rds
• [ ] tcga-gene-counts-rsem-expected_count-collapsed.rds
• [ ] rna-isoform-expression-rsem-tpm.rds
• [ ] methyl-m-values.rds
• [ ] methyl-cn-values.rds
• [ ] methyl-beta-values.rds
• [ ] independent-specimens.rnaseq.primary-plus.pre-release.tsv
• [ ] independent-specimens.rnaseq.primary.pre-release.tsv
• [ ] independent-specimens.rnaseq.relapse.pre-release.tsv

[Commit files]

• [ ] histologies.tsv
• [ ] efo-mondo-map.tsv
• [ ] ensg-hugo-pmtl-mapping.tsv
• [ ] uberon-map-gtex-group.tsv
• [ ] uberon-map-gtex-subgroup.tsv
• [ ] independent-specimens.methyl.primary-plus.eachcohort.tsv
• [ ] independent-specimens.methyl.primary-plus.tsv
• [ ] independent-specimens.methyl.primary.eachcohort.tsv
• [ ] independent-specimens.methyl.primary.tsv
• [ ] independent-specimens.methyl.relapse.eachcohort.tsv
• [ ] independent-specimens.methyl.relapse.tsv
• [ ] independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
• [ ] independent-specimens.rnaseqpanel.primary-plus.tsv
• [ ] independent-specimens.rnaseqpanel.primary.eachcohort.tsv
• [ ] independent-specimens.rnaseqpanel.primary.tsv
• [ ] independent-specimens.rnaseqpanel.relapse.eachcohort.tsv
• [ ] independent-specimens.rnaseqpanel.relapse.tsv
• [ ] independent-specimens.wgs.primary-plus.eachcohort.tsv
• [ ] independent-specimens.wgs.primary-plus.tsv
• [ ] independent-specimens.wgs.primary.eachcohort.tsv
• [ ] independent-specimens.wgs.primary.tsv
• [ ] independent-specimens.wgs.relapse.eachcohort.tsv
• [ ] independent-specimens.wgs.relapse.tsv
• [ ] independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.primary-plus.eachcohort.prefer.wxs.tsv
• [ ] independent-specimens.wgswxspanel.primary-plus.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.primary-plus.prefer.wxs.tsv
• [ ] independent-specimens.wgswxspanel.primary.eachcohort.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv
• [ ] independent-specimens.wgswxspanel.primary.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.primary.prefer.wxs.tsv
• [ ] independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv
• [ ] independent-specimens.wgswxspanel.relapse.prefer.wgs.tsv
• [ ] independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv

[Bed files and sample mapping]

• [ ] biospecimen_id_to_bed_map.txt
• [ ] ashion_exome_v2_targets_hg38_padded100.bed
• [ ] hg38_strelka.bed
• [ ] intersect_cds_lancet_strelka_mutect_WGS.bed
• [ ] intersect_strelka_mutect_WGS.bed
• [ ] nexterarapidcapture_exome_targetedregions_v1.2_hg38_100.bed
• [ ] S0274956_Padded_HG38.merged.bed
• [ ] S02972011_Covered_hg38_100.bed
• [ ] S04380110_Regions_hg38_100.bed
• [ ] S07604715_100bp_Padded.bed
• [ ] SeqCap_EZ_Exome_v2_Padded_HG38.merged.bed
• [ ] StrexomeLite_hg38_liftover_100bp_padded.bed
• [ ] Strexome_targets_intersect_sorted_padded100.GRCh38.bed
• [ ] TARGET_AML_NBL_WT_SeqVal79_attempt06_AllTracks_HG38_bed_expanded100.bed
• [ ] truseq-exome-targeted-regions-manifest-v1-2_hg38_100.bed
• [ ] wgs_canonical_calling_regions.hg38.bed
• [ ] WGS.hg38.lancet.300bp_padded.bed
• [ ] WGS.hg38.lancet.unpadded.bed
• [ ] WGS.hg38.mutect2.vardict.unpadded.bed
• [ ] WGS.hg38.strelka2.unpadded.bed
• [ ] WGS.hg38.vardict.100bp_padded.bed
• [ ] xgen-exome-research-panel-targets_hg38_ucsc_liftover.100bp_padded.sort.merged.bed

[File descriptions and notes]

• [ ] data-files-description.md
• [ ] release-notes.md

Any additional notes to add for discussion?

[jharenza]

Tumor only manifests

sd_bhjxbdqk-genomics_file_manifest.csv
sd_bhjxbdqk_cmi-genomics_file_manifest.csv
sd_bhjxbdqk_dgd_panel-genomics_file_manifest.csv

[jharenza]

now located https://github.com/rokitalab/OpenPedCan-Project/issues/5