add v18 release (#857)

* add v18 release * Update release-notes.md add pbta-histologies-base.tsv file to release notes Co-authored-by: Krutika Gaonkar <34580719+kgaonkar6@users.noreply.github.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
AlexsLemonade · Jan 12, 2021 · ce663d6 · ce663d6
1 parent 939b8c6
commit ce663d6
Show file tree

Hide file tree

Showing 2 changed files with 109 additions and 2 deletions.
diff --git a/doc/release-notes.md b/doc/release-notes.md
@@ -1,5 +1,112 @@
 # release notes
 ## current release
+### release-v18-20201123
+- release date: 2020-11-23
+- status: available
+- changes:
+  - Add `pbta-histologies-base.tsv` file, which does not contain `molecular_subtype` nor `integrated_diagnosis` and will be used for molecular subtyping modules in conjunction with data releases
+  - Add RNA independent specimen lists from [#795](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/795) and [#797](https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/797)
+  - Update DNA independent specimen lists per comment [here](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/750#issuecomment-691526896)
+  - Add LGAT fusion summary file from [#808](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/808) and [#830](https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/830)
+  - Update fusion files per comment [here](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/750#issuecomment-691529675)
+- Add kinase domain and reciprocal information to pbta-fusion-putative-oncogenic.tsv per [#812](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/812) and [#816](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/816) and [#821](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/821)
+  - Add 8 rRNA-depleted, total stranded RNA-Seq for tumors which previously had polyA sequencing performed: BS_FXJY0MNH, BS_KABQQA0T, BS_D7XRFE0R, BS_SHJA4MR0, BS_HE0WJRW6, BS_8QB4S4VA, BS_FN07P04C, BS_SB12W1XT per [#749](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/749)
+  - Update pbta-histologies.tsv:
+    - Add new RNA samples above
+    - Pull latest clinical data
+    - Add extent of tumor resection per [comment](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/750#issue-688364970)
+    - Rerun molecular subtyping modules to date
+    - Harmonize PNOC003 `pathology_diagnosis` to CBTN `pathology_diagnosis` and move original diagnosis to `pathology_free_text_diagnosis`
+    - Update CBTTC `cohort` to "CBTN"
+- folder structure:
+```
+data
+└── release-v18-20201123
+    ├── consensus_seg_annotated_cn_autosomes.tsv.gz
+    ├── consensus_seg_annotated_cn_x_and_y.tsv.gz
+    ├── data-files-description.md
+    ├── fusion_summary_embryonal_foi.tsv
+    ├── fusion_summary_ependymoma_foi.tsv
+    ├── fusion_summary_ewings_foi.tsv
+    ├── fusion_summary_lgat_foi.tsv
+    ├── independent-specimens.rnaseq.primary-plus-polya.tsv
+    ├── independent-specimens.rnaseq.primary-plus-stranded.tsv
+    ├── independent-specimens.wgs.primary-plus.tsv
+    ├── independent-specimens.wgs.primary.tsv
+    ├── independent-specimens.wgswxs.primary-plus.tsv
+    ├── independent-specimens.wgswxs.primary.tsv
+    ├── intersect_cds_lancet_strelka_mutect_WGS.bed
+    ├── intersect_cds_lancet_WXS.bed
+    ├── intersect_strelka_mutect_WGS.bed
+    ├── md5sum.txt
+    ├── pbta-cnv-cnvkit-gistic.zip
+    ├── pbta-cnv-cnvkit.seg.gz
+    ├── pbta-cnv-consensus-gistic.zip
+    ├── pbta-cnv-consensus.seg.gz
+    ├── pbta-cnv-controlfreec.tsv.gz
+    ├── pbta-fusion-arriba.tsv.gz
+    ├── pbta-fusion-putative-oncogenic.tsv
+    ├── pbta-fusion-recurrently-fused-genes-byhistology.tsv
+    ├── pbta-fusion-recurrently-fused-genes-bysample.tsv
+    ├── pbta-fusion-starfusion.tsv.gz
+    ├── pbta-gene-counts-rsem-expected_count.polya.rds
+    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
+    ├── pbta-gene-expression-kallisto.polya.rds
+    ├── pbta-gene-expression-kallisto.stranded.rds
+    ├── pbta-gene-expression-rsem-fpkm-collapsed.polya.rds
+    ├── pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds
+    ├── pbta-gene-expression-rsem-fpkm.polya.rds
+    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
+    ├── pbta-gene-expression-rsem-tpm.polya.rds
+    ├── pbta-gene-expression-rsem-tpm.stranded.rds
+    ├── pbta-histologies.tsv    
+    ├── pbta-histologies-base.tsv
+    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
+    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
+    ├── pbta-isoform-expression-rsem-tpm.polya.rds
+    ├── pbta-isoform-expression-rsem-tpm.stranded.rds
+    ├── pbta-mend-qc-manifest.tsv
+    ├── pbta-mend-qc-results.tar.gz
+    ├── pbta-snv-consensus-mutation.maf.tsv.gz
+    ├── pbta-snv-consensus-mutation-tmb-all.tsv
+    ├── pbta-snv-consensus-mutation-tmb-coding.tsv
+    ├── pbta-snv-lancet.vep.maf.gz
+    ├── pbta-snv-mutect2.vep.maf.gz
+    ├── pbta-snv-strelka2.vep.maf.gz
+    ├── pbta-snv-vardict.vep.maf.gz
+    ├── pbta-star-log-final.tar.gz
+    ├── pbta-star-log-manifest.tsv
+    ├── pbta-sv-manta.tsv.gz
+    ├── pbta-tcga-manifest.tsv
+    ├── pbta-tcga-snv-lancet.vep.maf.gz
+    ├── pbta-tcga-snv-mutect2.vep.maf.gz
+    ├── pbta-tcga-snv-strelka2.vep.maf.gz
+    ├── release-notes.md
+    ├── StrexomeLite_hg38_liftover_100bp_padded.bed
+    ├── StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.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
+    ├── WXS.hg38.100bp_padded.bed
+    ├── WXS.hg38.lancet.400bp_padded.bed
+    ├── intersected_whole_exome_agilent_designed_120_AND_tcga_6k_genes.Gh38.bed
+    ├── intersected_whole_exome_agilent_plus_tcga_6k_AND_tcga_6k_genes.Gh38.bed
+    ├── tcga_6k_genes.targetIntervals.Gh38.bed
+    ├── tcga_6k_genes.targetIntervals.bed
+    ├── tcga-snv-consensus-snv.maf.tsv.gz
+    ├── tcga-snv-mutation-tmb-all.tsv
+    ├── tcga-snv-mutation-tmb-coding.tsv
+    ├── whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.Gh38.bed
+    ├── whole_exome_agilent_1.1_refseq_plus_3_boosters.targetIntervals.bed
+    ├── whole_exome_agilent_designed_120.targetIntervals.Gh38.bed
+    ├── whole_exome_agilent_designed_120.targetIntervals.bed
+    ├── whole_exome_agilent_plus_tcga_6k.targetIntervals.Gh38.bed
+    └── whole_exome_agilent_plus_tcga_6k.targetIntervals.bed
+```
+
+## archived release
 ### release-v17-20200908
 - release date: 2020-09-11
 - status: available

diff --git a/download-data.sh b/download-data.sh
@@ -4,8 +4,8 @@ set -o pipefail
 
 # Use the OpenPBTA bucket as the default.
 URL=${OPENPBTA_URL:-https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/data}
-RELEASE=${OPENPBTA_RELEASE:-release-v17-20200908}
-PREVIOUS=${OPENPBTA_RELEASE:-release-v16-20200320}
+RELEASE=${OPENPBTA_RELEASE:-release-v18-20201123}
+PREVIOUS=${OPENPBTA_RELEASE:-release-v17-20200908}
 
 # Remove old symlinks in data
 find data -type l -delete