openvax neoantigen-vaccine-pipeline issues

openvax / neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Apache License 2.0

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issues

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Fixing RNA IndelRealigner rules: --intervals was (wrongly) not being triggered

#111 julia326 closed 6 years ago
0
Fixing how we compute the number of threads for DNA and RNA alignment

#110 julia326 closed 6 years ago
0
Subtract germline VCF from somatic VCFs

#109 iskandr opened 6 years ago
0
S04380110_Padded_grch37_with_M.bed not in reference archive

#108 davidroberson closed 5 years ago
3
rearranged the helper functions for threads and memory, added seq2hla

#107 iskandr closed 5 years ago
0
Add filtering germline variants by coverage (padded) file

#106 julia326 closed 6 years ago
0
Prepare Kallisto quantification for CIBERSORT

#105 iskandr opened 6 years ago
4
Try running POLYSOLVER

#104 iskandr opened 6 years ago
0
Identify driver variants

#103 iskandr closed 5 years ago
1
Generate Immunophenogram visualization

#102 iskandr opened 6 years ago
0
Add support for mm10

#101 julia326 closed 5 years ago
2
Add variant-calling-only mode

#100 julia326 closed 5 years ago
1
Adding ability to run in variant-calling-only mode

#99 julia326 closed 6 years ago
0
Fixing the way pipeline requests RAM for jobs

#98 julia326 closed 6 years ago
0
Pre-public pipeline updates

#97 julia326 closed 6 years ago
0
Make expected config YAML instead of JSON

#96 julia326 opened 6 years ago
1
Updates to README

#95 timodonnell closed 6 years ago
0
Make dbsnp/cosmic optional inputs

#94 julia326 opened 6 years ago
0
Run FusionCatcher on the tumor RNA

#93 iskandr opened 6 years ago
0
Identify deleterious mutations in antigen presentation pathways

#92 iskandr opened 6 years ago
4
Quantify MHC expression

#91 iskandr opened 6 years ago
0
Identify known driver variants from the somatic VCF

#90 iskandr opened 6 years ago
0
Add MHC predictor as an argument to the JSON config

#89 julia326 closed 5 years ago
1
Updating README for public use, adding RELEASING.md

#88 julia326 closed 6 years ago
0
Adding rules for HaplotypeCaller for normal BAMs

#87 julia326 closed 6 years ago
0
Add germline variant calling

#86 julia326 closed 6 years ago
1
Change copy-to-gcloud.sh to check if files exist

#85 julia326 closed 5 years ago
1
Lots of pipeline changes, largely in prep for splitting private/public Docker images:

#84 julia326 closed 6 years ago
0
Gzipping test data, so we never deal with materialized FASTQ files.

#83 julia326 closed 6 years ago
0
Adding a release script, small version increment for testing.

#82 julia326 closed 6 years ago
0
Version 0.1.0

#81 julia326 closed 6 years ago
0
Bunch of updates

#80 julia326 closed 6 years ago
0
Snakemake tries to recreate existing file

#79 julia326 opened 6 years ago
0
Copy overall Snakemake log out from container

#78 julia326 opened 6 years ago
0
Concurrent STAR alignment may sometimes not work

#77 julia326 opened 6 years ago
0
use psutil to get available memory and cores for each machine

#76 iskandr closed 6 years ago
2
Version Docker images

#75 julia326 closed 5 years ago
2
Adding some intermediate file paths to README

#74 julia326 closed 6 years ago
0
Moves notes txt into readme

#73 iskandr closed 6 years ago
0
moved test config to tests folder

#72 iskandr closed 6 years ago
0
Make it possible to specify libraries and lanes in config file

#71 iskandr opened 6 years ago
0
make LB tag in BAM specific to each sample, rather than constant 'ga'

#70 iskandr closed 6 years ago
0
Don't materialize decompressed .fastq.gz files

#69 iskandr closed 6 years ago
1
Don't copy FASTQs to output directory

#68 iskandr opened 6 years ago
0
Piping stdour/stderr STAR logs to a file

#67 julia326 closed 6 years ago
0
Fixing up some README things

#66 julia326 closed 6 years ago
0
Setting the pyensembl and reference peptide dirs to be under /reference-genome

#65 julia326 closed 6 years ago
0
Set the pyensembl cache directory to be /reference-genomes and not /outputs

#64 iskandr closed 6 years ago
0
Can it be killed?

#63 iskandr closed 6 years ago
2
Is it possible to check if -v dirs actually exist?

#62 iskandr opened 6 years ago
0

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