How To Buildup A Genome Assembly Workflow With Simple Scripts???
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10.0 years ago
HG ★ 1.2k

Hi Everyone,

I want to make a genome assembly workflow, from raw reads to draft genome. ( with Automatic QC/assembly/GapFilling/scaffolding).

For this i took various third party program and i have written some shell script to run one after another.

Now i want to make some user define flexibility with make file and i also want to pass some command line parameter. Can any one suggest me the how to make such a work flow. Which language will be better and some beginners guide how to generate make file

Thank you advance.

pipeline workflow • 2.6k views
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That's not clear to me: do you want to create a run a workflow using a Makefile ?. How about starting by reading some tutorials ?

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My basic algorithm that i am thinking it will be like : what ever program and parameter user will define according to that an executable file will generate and this file will run and give you result. And i discuss with some people they suggest me i can do through make file. Could you please let me know other idea.

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show us a draft of your Makefile and people will discuss it ?

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Till now i did not make any " make file" i put all the executable file (Fastqc/spades/mira/SSPACE/ PRICE), after that in shell script i pipe all the program one after another with specific data set. But here user cant define parameter they only run what ever i have written in shell script file. So now i want that user must have some flexibility for example if any one need only assebly he will run only that and he can install whole package in linux platform. Please let me know some idea how i can improve this idea.

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More over i have gone through this link but little bit confused how i can use such protocol in my work

How to organize a pipeline of small scripts together?

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