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Hi，the following error occurs when I run NeoFuse
`NeoFuse -1 /home/myname/data/neoantigen/1.fastq.gz -2 /home/myname/data/neoantigen/2.fastq.gz -s /home/myname/ref/neofuse/STAR_idx/ -g /home/myname/r…
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## COMPLETED
- [x] abacas (assigned @drpatelh)
- [x] agrvate (assigned @drpatelh)
- [x] bandage/image (assigned @drpatelh)
- [x] bismark/align (assigned @drpatelh)
- [x] bismark/deduplicat…
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commandline
`nextflow -c nfconf.txt run nf-core/hlatyping -profile awsbatch,test --awsqueue arn:aws:batch:eu-west-1:123456789:job-queue/test123aqueue --awsregion eu-west-1 --awscli /usr/local/bin/aw…
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I'm using Nextflow v21.02.0-edge, nf-core hlatyping pipeline v1.2.0 and Singularity v3.6.4-1.el7.
The `test_rna` and `test` profiles work as expected for me. However, running paired-end RNA fastq da…
ibwoo updated
2 years ago
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I apologise if this is trivial, but I checked other entries with this kind of error and I did not find a solution.
I am attaching the file that triggered the error. It is true that there are some e…
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Hi!
This issue is related to this one: https://github.com/nf-core/hlatyping/issues/111
I would like to be able to run the pipeline using just a fasta file as a reference. Internally the pipeline…
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``Hi!
I am trying to utlize your pipeline with hg19 instead of GRCh38. Because of this I am trying to recreate the yara references, but I have never used this tool before so I do not know what exa…
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This issue was discovered using a downsampled input data set.
If Optitype is unable to type an HLA gene, it reports a blank entry for that column.
This causes a failure in the extract HLA alle…
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when using docker file, It give me an error info, it seems to be the permission error of mkdir function. I googled and used the solution of add '--previliged=true', but it still doesn't work. My syste…
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### Description of bug
IndexError: list index out of range
### File that triggers the error
```tsv
file percent reads taxon_id taxon_name
NGS_0397…