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RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
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Differences in arguments between Dockerfile and on GitHub README #90

Closed ryanpe13002 closed 1 year ago

ryanpe13002 commented 2 years ago

To whom it may concern,

On the GitHub README file for arcasHLA, the option for determining if the input file is single- or paired-end is "--single : single-end reads (default: False)". However, when I download the Dockerfile at docker://jfx319/arcashla (obtained pursuant to this Issue raised on this Github repo: https://github.com/RabadanLab/arcasHLA/issues/24) and run "arcasHLA extract -h", it lists the available options as: "--paired paired-end reads, default: False".

I am wondering which is correct? I will run my script for the time being based on what's in the Dockerfile, but I am confused why there are two different approaches for the same option. Thanks so much!

olekskrav commented 1 year ago

Thanks for the question and sorry for the delayed reply.

For the best consistency between the documentation and the code, we recommend using our official Dockerfile located in the Docker folder.

As for the issue, in version 0.2.5 we changed the default behavior from single-end to paired-end reads, so now one should specify --single option to switch from the default paired-end mode to the single-end mode, while previously one had to specify --paired option to switch from the default single-end mode to the paired-end mode. It seems that the docker image you mentioned was built using the older version of arcasHLA, hence the discrepancy.