icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

icbi-lab/nextNEOpi Issues

License not recognized, Singularity image pull error
Updated a month ago1
Singularity image pull: "FATAL: the requested image was not found"
Closed 2 months ago3
Error executing process > 'install_IEDB (Install IEDB)'
Updated 3 months ago3
Does "nextNEOpi_1.4_resources.tar.gz" have the blast references required by nextNEOpi?
Closed 3 months ago2
mixMHC2pred not triggered when custom HLAs are used
Updated 4 months ago1
pVACseq (test_sample)` terminated with an error exit status (1)
Closed 4 months ago1
pVACtools_generate_protein_seq (test_sample)` terminated with an error exit status (1)
Closed 4 months ago5
Process `OptiType_RNA (test_sample)` terminated with an error exit status (1)
Closed 4 months ago13
Error executing process > 'pVACseq (sample1)'
Closed 4 months ago4
`pVACseq ` terminated with an error exit status (1)
Closed 4 months ago2
example of custom HLAs
Closed 4 months ago
Installation error with mamba
Closed 4 months ago14
'use_custom_hlas' not defined in the main script or the params file
Closed 4 months ago
HLA-HD silently fails if bowtie2 is not installed/loaded
Closed 4 months ago1
Process `get_vhla (test)` terminated with an error exit status (1)
Closed 4 months ago32
mkfifo: cannot create fifo : Operation not supported
Closed 4 months ago2
Error executing process "installVEPcache"
Closed 4 months ago7
Failed to run, issues related to pvacseq , etc
Closed 4 months ago5
Error in SetNmMdAndUqTags: Input must be coordinate-sorted
Closed 4 months ago5
nextNEO resources bundle installation issues
Closed 4 months ago4
Is .cram input format supported?
Closed 8 months ago1
amino acids sometimes doesn't match the reference or variant
Closed 9 months ago2
How could I improve this pipeline?
Updated 10 months ago
Process `installVEPcache (installVEPcache)` terminated with an error exit status (104)
Closed 10 months ago4
error message when run a test case
Closed 10 months ago12
Error executing process > 'gatherMutect2VCFs (sample2)'
Closed 10 months ago11
including SNV/indel calling on RNA-seq data
Closed 10 months ago1
Nextflow installation error
Closed a year ago3
pVACSeq chmod error
Closed a year ago4
Target regions bed file for TESLA patients 4,8,9
Closed a year ago3
NeoFuse: long running time
Closed a year ago4
make_uBAM process error
Closed a year ago13
Rerunning the pipeline from pVACseq
Closed a year ago5
Bwa terminated with an error exit status (137) -- Execution is retried
Closed a year ago5
Lacking VEP cache file Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Closed a year ago6
work folder
Closed a year ago1
CNNscoreVariant terminated with an error exit status (2)
Closed a year ago6
Pipeline complete but missing output file(s) for immunogenicity scoring
Closed a year ago3
Unable to parse config file: '/a/b/nextNEOpi/conf/params.config'
Closed a year ago7
yara_mapper doesn't run properly
Closed a year ago5
Can run on sensitive data cluster without internet access?
Closed a year ago3
Random error with NetMHCII
Closed a year ago4
-resume goes all the way back to SplitIntervals, make_uBAM and Bwa
Closed a year ago3
Issue with
Closed a year ago4
Provide test data
Closed a year ago5
Check if files exist, better error message than 'Cannot get property 'simpleName' on null object'
Closed a year ago2
nextNEOpi in DSL2/tool upgrades?
Closed a year ago1
No such file [...]/references/hg38/gdc/GRCh38.d1.vd1/fasta/hg38.len
Closed a year ago2
pVACsec fails on calculating manufacturability for MHC class II
Closed a year ago8
Not able to pull the images from apps-01.i-med.ac.at
Closed a year ago2