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How to run BBMap in a Linux shell for loop?
for I in ls (*.fastaq)  # mapping fastq files to a preset reference
do
    ./bbmap.sh $i
done

How to pass arguments after .sh call, what to write?

sequencing shell bash bbmap

Hello elvissober!

We believe that this post does not fit the main topic of this site.

Please look up bash loops. Do not open multiple questions addressing the same question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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