UGENE Forum - Modify workflow to fit 1 sample at a time

Sep 3^rd, 2020 at 7:59am

afina.m Offline
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Posts: 2

Hi all,

I am trying to create my own workflow as below:

1. Call 1 sample (AB1 file, forward and reverse)
2. Do quality trimming
3. Do de novo assembly using CAP3
4. Get output in fasta file

When I used the workflow, when I input all of my data, it able to do Step1 and Step2. However, at Step3, it gathers a few sample to get 1 assembly instead of 1 sample => 1 assembly.

I would like to modify the .uwl but it is not written in a common programming language (correct me if I'm wrong here). Therefore, is there a way to modify this so that the workflow will only read 1 sample at a time? Or do I have to execute the workflow using UGENE CLI where I can create my bash script?

And tips and advise is much appreciated.
Thank you in advance.

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Reply #1 - Sep 4^th, 2020 at 11:09am

Dmitrii Sukhomlinov Offline
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Russia

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Posts: 67

Hello,
There is a green plus button called "Add dataset" near the input files (see the attached picture). The datasets are processed as separate units, the workflow kinda runs several times (if you have 2 datasets - 2 times; if you have 3 datasets - 3 times)so, you can separate your input files into several datasets. Is that what you wanted?

Screenshot_1.jpg (182 KB | 162 )

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

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Reply #2 - Nov 12^th, 2020 at 4:11pm

afina.m Offline
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Posts: 2

Dmitrii Sukhomlinov wrote on Sep 4^th, 2020 at 11:09am:

Hello,
There is a green plus button called "Add dataset" near the input files (see the attached picture). The datasets are processed as separate units, the workflow kinda runs several times (if you have 2 datasets - 2 times; if you have 3 datasets - 3 times)so, you can separate your input files into several datasets. Is that what you wanted?

Hi Dmitrii,

Thank you for the reply. Yes, that is exactly what I was looking for.
However, as the number of samples that I have may be different (some project I have more than 20 samples and others might be less), is there any way to do this?
Instead of adding the dataset manually, can I do this by editing the .uwl?

Thank you in advance.

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Reply #3 - Nov 13^th, 2020 at 12:26pm

Dmitrii Sukhomlinov Offline
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Russia

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Posts: 67

Hello,

".uwl" is a special format, which was developed for UGENE and could be read and written by UGENE only. It's possible to change it by editing in any text editor (just open the file by, for example, notepad or notepad++), but if you do this UGENE posiibly won't figure the result file out and it may cause the data loss, so you can try to edit the ".uwl" file at your own risk.

If you still want to experiment with it, you may see in the file sections with the following id: "url-in" (see the attached picture) - this is the representations of datasets, by adding the part with this id you may add datasets.

Screenshot_1_001.png (22 KB | 148 )

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

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Reply #4 - Nov 16^th, 2020 at 9:59pm

ethan Offline
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Posts: 5

This is great!

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