Data release/add v5 release (AlexsLemonade#127)

* 📝 update release notes for v3

* 🔧 download script for v3-release

* 🔧 update release-notes.md for v5

* 🔧 update download-data.sh for v5

* ✨ add header for pbta-fusion-arriba.tsv.gz

* ✨ add header for pbta-fusion-starfusion.tsv.gz

* 🔧 update release-notes.md for v5, update folder structure

* 🔧 update release-notes.md; add rsem-isoform counts

doc/format/arriba-tsv-header.md

@@ -0,0 +1,29 @@
+```
+     1	gene1
+     2	gene2
+     3	strand1.gene.fusion.
+     4	strand2.gene.fusion.
+     5	breakpoint1
+     6	breakpoint2
+     7	site1
+     8	site2
+     9	type
+    10	direction1
+    11	direction2
+    12	split_reads1
+    13	split_reads2
+    14	discordant_mates
+    15	coverage1
+    16	coverage2
+    17	confidence
+    18	closest_genomic_breakpoint1
+    19	closest_genomic_breakpoint2
+    20	filters
+    21	fusion_transcript
+    22	reading_frame
+    23	peptide_sequence
+    24	read_identifiers
+    25	tumor_id
+    26	gene1--gene2
+    27	annots
+```

doc/format/starfusion-tsv-header.md

@@ -0,0 +1,28 @@
+```
+     1	FusionName
+     2	JunctionReadCount
+     3	SpanningFragCount
+     4	SpliceType
+     5	LeftGene
+     6	LeftBreakpoint
+     7	RightGene
+     8	RightBreakpoint
+     9	LargeAnchorSupport
+    10	FFPM
+    11	LeftBreakDinuc
+    12	LeftBreakEntropy
+    13	RightBreakDinuc
+    14	RightBreakEntropy
+    15	annots
+    16	CDS_LEFT_ID
+    17	CDS_LEFT_RANGE
+    18	CDS_RIGHT_ID
+    19	CDS_RIGHT_RANGE
+    20	PROT_FUSION_TYPE
+    21	FUSION_MODEL
+    22	FUSION_CDS
+    23	FUSION_TRANSL
+    24	PFAM_LEFT
+    25	PFAM_RIGHT
+    26	tumor_id
+```

doc/release-notes.md

@@ -1,5 +1,57 @@
 # release notes
 ## current release
+### release-v5-20190924
+- release date: 2019-09-24
+- status: available
+- changes:
+  - [Separated RNA-Seq files](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/121):
+    - Created separate RDS files for stranded and polyA RNA-Seq samples
+  - [new RNA-Seq counts files](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/14):
+    - Added RSEM count matrices for genes and transcripts
+  - [new ARRIBA file](https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/92#discussion_r324873300):
+    - Add `annots` column header which was removed during FusionAnnotator run
+  - [new SNV files](https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/114):
+    - Add Lancet VEP-annotated MAF
+    - Add VarDict VEP-annotated MAF
+  - [new BED interval files](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/3):
+    - Add WXS BED (same file used for each variant caller)
+    - Add WGS BED files for each variant caller
+    - Methods described [here](https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md).
+
+- folder structure:
+```
+data
+└── release-v5-20190924
+    ├── CHANGELOG.md
+    ├── md5sum.txt
+    ├── WGS.hg38.lancet.300bp_padded.bed
+    ├── WGS.hg38.lancet.unpadded.bed
+    ├── WGS.hg38.mutect2.unpadded.bed
+    ├── WGS.hg38.strelka2.unpadded.bed
+    ├── WGS.hg38.vardict.100bp_padded.bed
+    ├── WXS.hg38.100bp_padded.bed
+    ├── pbta-cnv-cnvkit.seg.gz
+    ├── pbta-cnv-controlfreec.seg.gz
+    ├── pbta-fusion-arriba.tsv.gz
+    ├── pbta-fusion-starfusion.tsv.gz
+    ├── pbta-histologies.tsv
+    ├── pbta-snv-mutect2.vep.maf.gz
+    ├── pbta-snv-strelka2.vep.maf.gz
+    ├── pbta-sv-lumpy.tsv.gz
+    ├── pbta-sv-manta.tsv.gz
+    ├── pbta-gene-expression-kallisto.polya.rds
+    ├── pbta-gene-expression-kallisto.stranded.rds
+    ├── pbta-gene-expression-rsem-fpkm.polya.rds
+    ├── pbta-gene-expression-rsem-fpkm.stranded.rds
+    ├── pbta-gene-counts-rsem-expected_count.polya.rds
+    ├── pbta-gene-counts-rsem-expected_count.stranded.rds
+    ├── pbta-isoform-counts-rsem-expected_count.polya.rds
+    ├── pbta-isoform-counts-rsem-expected_count.stranded.rds
+    ├── pbta-snv-lancet.vep.maf.gz
+    └── pbta-snv-vardict.vep.maf.gz
+```
+
+## archived release
 ### release-v4-20190909
 - release date: 2019-09-10
 - status: available
@@ -28,7 +80,8 @@ data
     ├── pbta-snv-mutect2.vep.maf.gz
     ├── pbta-snv-strelka2.vep.maf.gz
     ├── pbta-sv-lumpy.tsv.gz
-    └── pbta-sv-manta.tsv.gz
+    ├── pbta-sv-manta.tsv.gz
+    └── README.md
 ```
 
 ## archived release
@@ -104,3 +157,7 @@ data
     ├── strelka2.maf.gz
     └── tumor-normal-pair.tsv
 ```
+
+
+
+

download-data.sh

@@ -4,7 +4,7 @@ set -o pipefail
 
 # Use the OpenPBTA bucket as the default.
 URL=${URL:-https://s3.amazonaws.com/kf-openaccess-us-east-1-prd-pbta/data}
-RELEASE=${RELEASE:-release-v4-20190909}
+RELEASE=${RELEASE:-release-v5-20190924}
 
 # The md5sum file provides our single point of truth for which files are in a release.
 curl --create-dirs $URL/$RELEASE/md5sum.txt -o data/$RELEASE/md5sum.txt -z data/$RELEASE/md5sum.txt