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x-ref: https://github.com/nf-core/tools/issues/267
Proof of concept implementation.
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Hi,
Why I don't get HLA typing of all the genes (A, B and C) in a single run? Rather, I have to run multiple times to get that (as shown below). I wonder if its bug.
And, do you think removing d…
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**Version info**
- bcbio version : 1.1.5
Hi Bcbio Team,
Currently, I am running HLA typing using OptiType. I use BAM as input `aligner: false`, since I don't want to redo the mapping step to f…
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Hello, I'm a new user and excited to try out this tool. I am getting an error in the 1st step. I have already installed the pysam module (I can import it via the python command line) however I'm still…
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Hello,
kind of stuck, I installed optitype with conda. Had to use python v2.7 (miniconda2) in order to install it.
When I run this command:
```
.../miniconda2/bin/OptiTypePipeline.py -i sample…
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### Query
To put it simple, I just hope to know how to bind/mount a host folder to a folder in container system if the software I am gonna run in the container have an output argument? **In another…
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**Version info**
- bcbio-nextgen==1.2.4
- Ubuntu 20.04.1 LTS
**To Reproduce**
Exact bcbio command you have used:
```
sudo apt-get -y update
sudo apt-get -y install aptitude
sudo DEBIAN_FRO…
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Hi, I have a problem.
How can I solve the problem?
```
[0;35m[nf-core/hlatyping] Pipeline completed with errors
Error executing process > 'remap_to_hla (1)'
Caused by:
Process `remap_to_h…
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Hello
I have a set of vcf files (SNVs) from patients who have responded to chemotherapy versus a set of patients who have not responded.
I want to quantify the neoantigen load in the tumors ,can…
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I am currently using Conda for next flow with following version:
Version: 20.04.1 build 5335
Created: 03-05-2020 19:37 UTC (15:37 EDT)
System: Mac OS X 10.14.6
Runtime: Groovy 2.5.8 on Ope…