REAPR-PIPELINE(1)

💖 REAPR-PIPELINE(1) 💖

okay bestie, welcome to reapr-pipeline — it's the manual page for running the whole REAPR pipeline, and honestly? we're gonna get you through this together, no cap 🫶

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✨ NAME ✨

reapr-pipeline — run the REAPR pipeline 🧚 (yes that's the whole job description and it's serving)

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🌸 SYNOPSIS 🌸

reapr pipeline [options] <assembly.fa> <in.bam> <outdirectory>
[perfectmapprefix]

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💅 DESCRIPTION 💅

[perfectmapprefix] is optional, bestie — it's literally the prefix you used back when the task perfectmap was run. that's it, that's the whole thing 💖

and lowkey important: the pipeline assumes that the reads sitting in <in.bam> are 'innies' 🔥 aka the correct orientation is reads in a pair pointing towards each other, like this:

--→ ←--

so if your reads are outies... tragic, that's not this vibe. 🙈

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🎀 OPTIONS 🎀

• -stats|fcdrate|score|break option=value — okay so you can pass options straight through to stats, fcdrate, score or break if you wanna change their default settings ✨ and yes, you can use this multiple times so you can stack more than one option. like, for real for real:

-stats i=100 -stats j=1000

and if some option has no value at all? just use 1. no thoughts, head empty, just:

-break b=1

• -fcdcut <float> — this sets the fcdcutoff that gets used when running score. by default, fcdrate is run to figure out that cutoff for you 👑 but the second you use this option? it skips fcdrate entirely and just uses the value you gave it. bold, decisive, main character energy 💅
• -x — so by default the pipeline writes out a bash script to run all the pipeline stages 📜 but with -x, it stops that script from being run. just... sits there. unrun. iconic behaviour honestly.

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🔍 SEE ALSO 🔍

• reapr(1) 🌈

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and that's the whole page, bestie! go forth and pipeline responsibly 🦋💜

REAPR-PIPELINE(1) — mwah, that's the manual name, version, date and everything, all wrapped up in one lil sign-off from me to you 🎀💖✨