icbi-lab nextNEOpi issues

icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

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Singularity image pull: "FATAL: the requested image was not found"

#78 CSree closed 2 minutes ago
1
Error executing process > 'install_IEDB (Install IEDB)'

#77 Xiao-Zhong opened 2 weeks ago
3
Does "nextNEOpi_1.4_resources.tar.gz" have the blast references required by nextNEOpi?

#76 Xiao-Zhong closed 3 weeks ago
2
pVACseq (test_sample)` terminated with an error exit status (1)

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

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

#73 DecodeGenome closed 1 month ago
13
example of custom HLAs

#72 mantczakaus closed 1 month ago
0
mixMHC2pred not triggered when custom HLAs are used

#71 mantczakaus opened 4 months ago
1
'use_custom_hlas' not defined in the main script or the params file

#70 mantczakaus closed 1 month ago
0
Is .cram input format supported?

#69 yh154 closed 6 months ago
1
amino acids sometimes doesn't match the reference or variant

#68 zktuong closed 6 months ago
2
Process `get_vhla (test)` terminated with an error exit status (1)

#67 rashidma closed 2 months ago
32
`pVACseq ` terminated with an error exit status (1)

#66 sasi-arunachalam closed 1 month ago
2
mkfifo: cannot create fifo : Operation not supported

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

#64 gri11 opened 7 months ago
0
Error executing process "installVEPcache"

#63 ryao-mdanderson closed 2 months ago
7
HLA-HD silently fails if bowtie2 is not installed/loaded

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

#61 zktuong closed 7 months ago
1
Error executing process > 'pVACseq (sample1)'

#60 gri11 closed 1 month ago
4
Failed to run, issues related to pvacseq , etc

#59 CSree closed 2 months ago
5
nextNEO resources bundle installation issues

#58 bbmorris1 closed 2 months ago
4
Process `installVEPcache (installVEPcache)` terminated with an error exit status (104)

#57 rashidma closed 7 months ago
4
pVACSeq chmod error

#56 zktuong closed 8 months ago
4
NeoFuse: long running time

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

#54 mantczakaus closed 9 months ago
3
Error executing process > 'gatherMutect2VCFs (sample2)'

#53 amoschoomy closed 7 months ago
11
error message when run a test case

#52 ryao-mdanderson closed 7 months ago
12
Nextflow installation error

#51 bbmorris1 closed 9 months ago
3
Bwa terminated with an error exit status (137) -- Execution is retried

#50 amoschoomy closed 9 months ago
5
make_uBAM process error

#49 gri11 closed 9 months ago
13
Lacking VEP cache file Homo_sapiens.GRCh38.dna.toplevel.fa.gz

#48 wwoskie closed 9 months ago
6
work folder

#47 amoschoomy closed 9 months ago
1
CNNscoreVariant terminated with an error exit status (2)

#46 rashidma closed 9 months ago
6
Pipeline complete but missing output file(s) for immunogenicity scoring

#45 amoschoomy closed 9 months ago
3
update bioconda channels link

#44 wwoskie closed 9 months ago
1
Installation error with mamba

#43 fredsamhaak closed 1 month ago
14
Unable to parse config file: '/a/b/nextNEOpi/conf/params.config'

#42 rashidma closed 10 months ago
7
Error in SetNmMdAndUqTags: Input must be coordinate-sorted

#41 gri11 closed 2 months ago
5
yara_mapper doesn't run properly

#40 mantczakaus closed 10 months ago
5
Rerunning the pipeline from pVACseq

#39 mantczakaus closed 9 months ago
5
add testdata_batchFile_FASTQ.csv

#38 gri11 closed 9 months ago
1
Can run on sensitive data cluster without internet access?

#37 richelbilderbeek closed 11 months ago
3
Check if files exist, better error message than 'Cannot get property 'simpleName' on null object'

#36 richelbilderbeek closed 11 months ago
2
nextNEOpi in DSL2/tool upgrades?

#35 mantczakaus closed 11 months ago
1
No such file [...]/references/hg38/gdc/GRCh38.d1.vd1/fasta/hg38.len

#34 richelbilderbeek closed 12 months ago
2
Provide test data

#33 richelbilderbeek closed 11 months ago
5
Issue with

#32 mulqueenr closed 11 months ago
4
Random error with NetMHCII

#31 mantczakaus closed 11 months ago
4
-resume goes all the way back to SplitIntervals, make_uBAM and Bwa

#30 mantczakaus closed 11 months ago
3
pVACsec fails on calculating manufacturability for MHC class II

#29 mantczakaus closed 1 year ago
8