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meglab-metagenomics / amrplusplus_v2

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data
http://megares.meglab.org/
MIT License
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Host index uncertainty #9

Closed MatteoSchiavinato closed 2 years ago

MatteoSchiavinato commented 4 years ago

Hi,

I am running the main_AmrPlusPlus_v2_withRGI_Kraken.nf workflow, and I'm doing it with --host_index.

I'm not sure I'm doing things correctly, since the usage page says --index and not --host_index.

I just wanted to bring this up, because the --help says --host_index, from the script.

I would suggest a slight modification of the option, that could be easier to understand. Instead of having to declare all the index file using the * wildcard, it would be easier if people had to declare the index prefix including the path (like in bowtie2 for example).

That way, the --host option would be automatically checked for the existence of an index by checking if it has the index files with the same prefix, and the user would only have to index the FASTA reference file using bwa index ${REF}.

EnriqueDoster commented 2 years ago

Hi @MatteoSchiavinato, thanks for the feedback! I see what you mean and I'll try it out on our next update. For now, we updated the usage page.