Question: Trimmomatic in Galaxy
gravatar for dineli_karunathilaka
2.2 years ago by
dineli_karunathilaka10 wrote:


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

ADD COMMENTlink modified 2.2 years ago by peter.briggs20 • written 2.2 years ago by dineli_karunathilaka10
gravatar for peter.briggs
2.2 years ago by
United Kingdom
peter.briggs20 wrote:


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.



ADD COMMENTlink written 2.2 years ago by peter.briggs20

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="">} ERROR 2016-09-28 17:42:06,426 Failed to execute scheduled workflow.

Please refer the attached workflow.


ADD REPLYlink written 2.2 years ago by dineli_karunathilaka10

Hello, You are working at, 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

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k

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. Error message

This is the shared link of my history:

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


If you need anything else let me know.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by dineli_karunathilaka10

Hi Jen,

Is there any update on this??

ADD REPLYlink written 2.2 years ago by dineli_karunathilaka10
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson25k

Hello Jen The Github repository in the Tool Shed has now been updated to - thanks for letting me know that it was wrong previously. Best wishes, Peter

ADD REPLYlink written 2.2 years ago by peter.briggs20

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 REPLYlink written 2.2 years ago by dineli_karunathilaka10
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