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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Annotate VAFs in the all-passing-variants file

#161 timodonnell closed 3 months ago
1
Creating a tmp subfolder if it does not exist, in the workdir; bumping pipeline version

#160 julia326 closed 3 months ago
0
Making most output files Snakemake-temp, so that the pipeline cleans up after itself as it goes

#159 julia326 closed 4 months ago
0
Bump jinja2 from 3.0.3 to 3.1.4

#158 dependabot[bot] opened 4 months ago
0
Adding mhcflurry, upgrading Python stack

#157 julia326 closed 4 months ago
0
report bug

#156 Cosmos9526 opened 5 months ago
0
Use NetMHC locally in pipeline

#155 hjaysong opened 9 months ago
0
Runable pipeline mhc 2

#154 Emon46 closed 9 months ago
0
Update to use modern tooling

#153 julia326 closed 10 months ago
1
Error when running test samples

#152 staracode closed 1 year ago
0
Relative path issue when running not in the repo directory

#151 gongyixiao opened 2 years ago
0
Overriding yaml file paths using parameters in dockerless mode

#150 gongyixiao opened 2 years ago
0
Failed to call strelka2

#149 marcogao2019 opened 3 years ago
0
Updating the Dockerfile (fixing a couple of recent breakages)

#148 julia326 closed 4 years ago
0
docker building failed using build.sh command

#147 joshuabhk opened 4 years ago
2
Making Excel output from Vaxrank optional.

#146 julia326 closed 4 years ago
0
Non-parallel IndelRealigner sometimes fails

#145 julia326 opened 5 years ago
0
Add chimeric alignments to STAR

#144 iskandr opened 5 years ago
0
Rolls in QC metrics file into pipeline container

#143 julia326 closed 5 years ago
0
Add Manta for identifying candidate larger indels

#142 iskandr opened 5 years ago
2
--run-qc only works with --qc-metrics-file for now

#141 julia326 closed 5 years ago
1
check if files exist before trying to copy them to gcloud

#140 iskandr closed 5 years ago
0
Remove pyensembl install rules

#139 julia326 closed 5 years ago
0
Adding a QC script that checks Picard's CollectHsMetrics and DuplicationMetrics

#138 julia326 closed 5 years ago
0
Add grch38 support

#137 julia326 closed 5 years ago
0
Add strelka2 to pipeline

#136 julia326 opened 5 years ago
4
Fix picard "no space left on device" error (when running SortSam)

#135 julia326 closed 5 years ago
0
Setting workdir explicitly in call to snakemake.snakemake

#134 julia326 closed 5 years ago
0
Use subprocess.call to copy files with cp instead of shutil.copy2

#133 julia326 closed 5 years ago
0
Make sure initial input files fully copied over

#132 julia326 opened 5 years ago
0
Added two print statements

#131 iskandr closed 5 years ago
0
Adding fastqc rule, upping version to 0.4.0.

#130 julia326 closed 5 years ago
0
Prioritize mutect-strelka Vaxrank over mutect2 jobs

#129 julia326 opened 5 years ago
0
Upload all-passing-variants CSV to GCloud as part of copy script

#128 julia326 closed 6 years ago
0
Check config file for obvious mistakes

#127 iskandr opened 6 years ago
0
Add argument to STAR to save unmapped RNA reads

#126 iskandr closed 5 years ago
2
Long-running steps

#125 iskandr opened 6 years ago
0
Don't explicitly use PyEnsembl install

#124 iskandr closed 5 years ago
2
How do we make `copy-to-gcloud.sh` a part of the pipeline?

#123 iskandr opened 6 years ago
1
Run STAR in "two pass mode" to detect novel splice junctions

#122 iskandr opened 6 years ago
0
Saved unmapped RNA reads in SAM/BAM output

#121 iskandr opened 6 years ago
0
QC tools for RNA and DNA

#120 julia326 opened 6 years ago
1
Ensembl 75 (human) and Ensembl 93 (mouse) always get installed with pyensembl

#119 iskandr closed 5 years ago
4
Alternative config format for sequencing data

#118 iskandr opened 6 years ago
0
Fixing TMPDIR path in Mark Duplicates rule.

#117 julia326 closed 6 years ago
0
Fix IndelRealigner rules around BAM index files

#116 julia326 closed 6 years ago
0
Upgrade vaxrank

#115 julia326 closed 6 years ago
0
Upgrading Vaxrank version, adding a Pyensembl mouse install.

#114 julia326 closed 6 years ago
0
Fairly large refactor: adding support for arbitrary reference genome

#113 julia326 closed 6 years ago
0
Adding the ability to run outside of Docker

#112 julia326 closed 6 years ago
0