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openvax
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neoantigen-vaccine-pipeline
Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Apache License 2.0
75
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25
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Add command to make reference genome & output dir world writeable to README (+ explanation)
#61
iskandr
closed
6 years ago
0
Add explanation `docker login` error to README
#60
iskandr
closed
6 years ago
0
More Docker-related things
#59
julia326
closed
6 years ago
0
Removing a couple unneeded files
#58
julia326
closed
6 years ago
0
More pipeline changes
#57
julia326
closed
6 years ago
0
More toward dockerizing pipeline
#56
julia326
closed
6 years ago
0
Have a flag for whether to parallelize IndelRealigner
#55
julia326
closed
6 years ago
1
quantify RNA transcripts using kallisto
#54
timodonnell
opened
6 years ago
3
WIP: Dockerizing the pipeline
#53
julia326
closed
6 years ago
0
Auto-populate variant review Google spreadsheet
#52
iskandr
opened
6 years ago
0
Copy to GCloud script
#51
julia326
closed
6 years ago
0
Update Snakemake unit test
#50
julia326
closed
6 years ago
0
Updating the Vaxrank rule to run for an arbitrary set of VCFs
#49
julia326
closed
6 years ago
0
Turn notes.txt into a Dockerfile
#48
iskandr
closed
6 years ago
1
Test- and test-data-related changes
#47
julia326
closed
6 years ago
0
Adding a pip requirements file and a Conda spec file.
#46
julia326
closed
6 years ago
0
Add a pipeline test that actually runs on the IDH1 test data
#45
julia326
opened
6 years ago
0
Turn the Snakemake setup into a Dockerfile
#44
julia326
closed
6 years ago
1
Add vaxrank rule for only mutect/strelka
#43
julia326
closed
6 years ago
1
Adding a unit test to check rule graph validity
#42
julia326
closed
6 years ago
0
Preprocess reference FASTA if necessary
#41
julia326
closed
6 years ago
1
Use Google client libraries for bucket access
#40
julia326
opened
6 years ago
0
Add support for copying input FASTQs from gs:// links
#39
julia326
closed
6 years ago
0
Get Snakemake working with gs:// links
#38
julia326
closed
6 years ago
0
Automate creation of IGV session
#37
julia326
opened
6 years ago
0
Add a step to back up final results to gcloud
#36
julia326
opened
6 years ago
0
Several DNA IndelRealigner changes
#35
julia326
closed
6 years ago
0
Make pipeline work with IDH1 fastq
#34
julia326
closed
6 years ago
0
Run BAM post-processing per lane before merging and running per sample
#33
iskandr
opened
6 years ago
0
Add ABRA2 as an indel realigner
#32
iskandr
opened
6 years ago
0
Run IndelRealigner jointly on tumor/normal
#31
julia326
closed
6 years ago
1
Add a rule to index final DNA/RNA BAMs
#30
julia326
closed
6 years ago
0
Convert notes.txt to repo README
#29
julia326
closed
6 years ago
1
Increasing RNA IndelRealigner heap size to 20g
#28
julia326
closed
6 years ago
0
Add a rule to start with an unsorted/unaligned BAM
#27
julia326
opened
6 years ago
0
Generate vaxrank reports with and without Mutect2
#26
julia326
closed
6 years ago
1
added IPython notebook for synthesizing IDH1 R132H reads
#25
iskandr
closed
6 years ago
0
Fix thread counts, memory resources tags
#24
julia326
closed
6 years ago
0
Fixing the way SM tags are set in DNA read groups
#23
julia326
closed
6 years ago
0
Different SM tags in final BAMs confuses mutect2
#22
julia326
closed
6 years ago
0
Add vaxrank with mutect2
#21
julia326
closed
6 years ago
0
Add MultiQC
#20
iskandr
opened
6 years ago
2
Add local-wgs1 benchmark data
#19
timodonnell
opened
6 years ago
4
Filter VCFs by coverage file before running vaxrank
#18
julia326
opened
6 years ago
2
Add seq2hla support
#17
julia326
opened
6 years ago
1
Get Snakemake GUI working on the PGV project node
#16
julia326
opened
6 years ago
0
STAR alignment logs print to stdout
#15
julia326
closed
6 years ago
0
Removing configfile path from Snakefile
#14
julia326
closed
6 years ago
0
Full code PR
#13
tavinathanson
closed
6 years ago
0
Add vaxrank
#12
julia326
closed
6 years ago
0
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