icbi-lab nextNEOpi issues

icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

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MHCFlurry temp file error

#85 gilsonmm opened 5 hours ago
0
New version of nextNEOpi

#84 mantczakaus opened 1 month ago
0
Problems with cache

#83 mantczakaus opened 1 month ago
0
Running nextNEOpi on big WGS data

#82 mantczakaus opened 1 month ago
2
Using the pipeline on cell line data

#81 GMFranceschini closed 1 month ago
1
--WES false error

#80 gilsonmm closed 1 month ago
8
License not recognized, Singularity image pull error

#79 CSree closed 2 months ago
2
Singularity image pull: "FATAL: the requested image was not found"

#78 CSree closed 4 months ago
3
Error executing process > 'install_IEDB (Install IEDB)'

#77 Xiao-Zhong closed 2 months ago
4
Does "nextNEOpi_1.4_resources.tar.gz" have the blast references required by nextNEOpi?

#76 Xiao-Zhong closed 5 months ago
2
pVACseq (test_sample)` terminated with an error exit status (1)

#75 DecodeGenome closed 6 months ago
1
pVACtools_generate_protein_seq (test_sample)` terminated with an error exit status (1)

#74 DecodeGenome closed 6 months ago
5
Process `OptiType_RNA (test_sample)` terminated with an error exit status (1)

#73 DecodeGenome closed 6 months ago
13
example of custom HLAs

#72 mantczakaus closed 6 months ago
0
mixMHC2pred not triggered when custom HLAs are used

#71 mantczakaus opened 9 months ago
1
'use_custom_hlas' not defined in the main script or the params file

#70 mantczakaus closed 6 months ago
0
Is .cram input format supported?

#69 yh154 closed 10 months ago
1
amino acids sometimes doesn't match the reference or variant

#68 zktuong closed 11 months ago
2
Process `get_vhla (test)` terminated with an error exit status (1)

#67 rashidma closed 6 months ago
32
`pVACseq ` terminated with an error exit status (1)

#66 sasi-arunachalam closed 6 months ago
2
mkfifo: cannot create fifo : Operation not supported

#65 rashidma closed 6 months ago
2
How could I improve this pipeline?

#64 gri11 opened 1 year ago
0
Error executing process "installVEPcache"

#63 ryao-mdanderson closed 6 months ago
7
HLA-HD silently fails if bowtie2 is not installed/loaded

#62 dmgie closed 6 months ago
1
including SNV/indel calling on RNA-seq data

#61 zktuong closed 1 year ago
1
Error executing process > 'pVACseq (sample1)'

#60 gri11 closed 6 months ago
4
Failed to run, issues related to pvacseq , etc

#59 CSree closed 6 months ago
5
nextNEO resources bundle installation issues

#58 bbmorris1 closed 6 months ago
4
Process `installVEPcache (installVEPcache)` terminated with an error exit status (104)

#57 rashidma closed 1 year ago
4
pVACSeq chmod error

#56 zktuong closed 1 year ago
4
NeoFuse: long running time

#55 fredsamhaak closed 1 year ago
4
Target regions bed file for TESLA patients 4,8,9

#54 mantczakaus closed 1 year ago
3
Error executing process > 'gatherMutect2VCFs (sample2)'

#53 amoschoomy closed 1 year ago
11
error message when run a test case

#52 ryao-mdanderson closed 1 year ago
12
Nextflow installation error

#51 bbmorris1 closed 1 year ago
3
Bwa terminated with an error exit status (137) -- Execution is retried

#50 amoschoomy closed 1 year ago
5
make_uBAM process error

#49 gri11 closed 1 year ago
13
Lacking VEP cache file Homo_sapiens.GRCh38.dna.toplevel.fa.gz

#48 wwoskie closed 1 year ago
6
work folder

#47 amoschoomy closed 1 year ago
1
CNNscoreVariant terminated with an error exit status (2)

#46 rashidma closed 1 year ago
6
Pipeline complete but missing output file(s) for immunogenicity scoring

#45 amoschoomy closed 1 year ago
3
update bioconda channels link

#44 wwoskie closed 1 year ago
1
Installation error with mamba

#43 fredsamhaak closed 6 months ago
14
Unable to parse config file: '/a/b/nextNEOpi/conf/params.config'

#42 rashidma closed 1 year ago
7
Error in SetNmMdAndUqTags: Input must be coordinate-sorted

#41 gri11 closed 6 months ago
5
yara_mapper doesn't run properly

#40 mantczakaus closed 1 year ago
5
Rerunning the pipeline from pVACseq

#39 mantczakaus closed 1 year ago
5
add testdata_batchFile_FASTQ.csv

#38 gri11 closed 1 year ago
1
Can run on sensitive data cluster without internet access?

#37 richelbilderbeek closed 1 year ago
3
Check if files exist, better error message than 'Cannot get property 'simpleName' on null object'

#36 richelbilderbeek closed 1 year ago
2