Trimmomatic in Galaxy

Question: Trimmomatic in Galaxy

2.2 years ago by

dineli_karunathilaka • 10

dineli_karunathilaka • 10 wrote:

Hi,

Is there a way to change the order of the ILLUMINACLIP in Galaxy? In galaxy it is always performed initially.

Ex: I need to perform CROP action first, then comes the ILLUMINACLIP.

Thanks in advance.

Regards, Dineli

order tool-form options trimmomatic illuminaclip • 1.3k views

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modified 2.2 years ago by peter.briggs • 20 • written 2.2 years ago by dineli_karunathilaka • 10

2.2 years ago by

peter.briggs • 20

United Kingdom

peter.briggs • 20 wrote:

Hello

I'm the author and maintainer of the Trimmomatic tool in the Galaxy toolshed, which wraps Anthony Bolger's Trimmomatic program. In designing the tool we decided that we would force the ILLUMINACLIP operation to always be performed first (if specified), as the Trimmomatic documentation states "[i]t is recommended in most cases that adapter clipping, if required, is done as early as possible, since correctly identifying adapters using partial matches is more difficult".

In cases where you've decided you need to perform other operations before ILLUMINACLIP, we'd suggest the same procedure that Jen suggests in her answer i.e.:

Run the Trimmomatic tool once on your initial Fastq pair, specifying just the "pre-ILLUMINACLIP" operations (e.g. CROP, in your example)
Run the tool again on the output of that step to do ILLUMINACLIP (plus any additional operations)

For the second run you'll need to use the "Trimmomatic on ... (R1 paired)" and "Trimmomatic on ... (R2 paired)" outputs from the first run as input.

HTH

Peter

ADD COMMENT • link written 2.2 years ago by peter.briggs • 20

Thanks Peter for the explanation.

I did as you and Jen suggested but i'm getting the below error. Exception: Workflow evaluation problem - failed to find output_name fastq_out_r1_paired in step_outputs {u'fastq_out_paired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3c0c7ef850="">, u'fastq_out_unpaired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3c240c0f50="">} galaxy.workflow.run ERROR 2016-09-28 17:42:06,426 Failed to execute scheduled workflow.

Please refer the attached workflow.

workflow

ADD REPLY • link written 2.2 years ago by dineli_karunathilaka • 10

Hello, You are working at http://usegalaxy.org, correct? If working there or can replicate this issue there - please send in a bug report from the history you ran this workflow against. Leave all datasets undeleted. In the bug report comments include a Share link to this workflow. I'll take a look and see where the problem is.. it looks a bit like real issue - but more feedback once we have a look. Jen

How to create workflow share link: https://wiki.galaxyproject.org/Learn/Share
How to submit a bug: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

I have my own galaxy instance. But I tried replicating the issue on 'usegalaxy' as well. Problem is it never display an error on the history instead it publishes an error message on the galaxy dashboard. (refer the image) Thus I am unable to report it as a bug. Since I got the internal server error message I believe I was able to generate the issue on the public instance.

This is the shared link of my history: https://usegalaxy.org/u/xxxadmindk/h/trimmomatic-test

In my local instance i can access the server log so I was able to identify what the real exception was. I will publish the whole error below for your reference.Exception-log

exception

If you need anything else let me know.

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by dineli_karunathilaka • 10

Hi Jen,

Is there any update on this??

ADD REPLY • link written 2.2 years ago by dineli_karunathilaka • 10

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

What you describe is the fixed order of the operations performed by the tool as currently wrapped for Galaxy. For your use case, perhaps run the sequences through the tool twice? Run once through to crop, then again to do just the clip? The two tools (and other others you are using for routine QA) could be put into a workflow to make this less tedious to execute in the future - or individual or multiple files going forward. To recover disk space once finished with a confirmed result that meets your needs, the intermediate fastq files can be permanently deleted.

I made an enhancement request on your behalf directly to the tool author with a link to this post. The github repository link is currently incorrect in the Tool Shed - and I let them know about that, too. They may post back here with a ticket to track the request or with other comments.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jen The Github repository in the Tool Shed has now been updated to https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/tools/trimmomatic - thanks for letting me know that it was wrong previously. Best wishes, Peter

ADD REPLY • link written 2.2 years ago by peter.briggs • 20

Thank you very much for your feedback Jen.

I am a newbie to Galaxy thus I have several questions. Are you are suggesting to use 2 trimmomatc tools?(1 for crop and other for clip) If so how can I connect the 2 tools? I mean, output from the first trimmomatic should use as the input for the 2nd tool isn't it? I tried several ways but was unable to get the desired output. Can you please explain me how to do it? I'm using a paired data set as the input. Appreciate your help.

ADD REPLY • link written 2.2 years ago by dineli_karunathilaka • 10

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