Question: Changing datatype of multiple datasets in batch
1
gravatar for ropolocan
10 months ago by
ropolocan30
Canada
ropolocan30 wrote:

Hello everyone,

I have uploaded a number of *.fastq.gz files to a Galaxy instance. Unfortunately, I forgot to change the format of the files to fastqsanger. I know that I can change the datatype to fastqsanger by going Edit Attributes -> Datatype, and then assigning a new type from the dropdown list. How can I do this for multiple datasets without having to individually change them manually?

Your help will be much appreciated!!

format batch jobs datatypes • 313 views
ADD COMMENTlink modified 10 months ago by Guy Reeves1.0k • written 10 months ago by ropolocan30
3
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

An enhancement request for additional batch dataset changes, including datatype reassignment, is ticketed and under consideration. Please follow progress here: https://github.com/galaxyproject/galaxy/issues/3195

For now, the method you describe is the available option. Metadata changes are per-dataset.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 months ago by Jennifer Hillman Jackson24k

Thank you so much for your answer, Jen! I will be following the progress of this request on GitHub.

ADD REPLYlink modified 10 months ago • written 10 months ago by ropolocan30
0
gravatar for Guy Reeves
10 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI Might it be possible to set up a short workflow and input all your datasets in a list allowing you to do 100s at a time easily . Maybe: Input dataset> then a tool which will recognise the current datatype but will output essentially the same data but where the 'Configure Output: >Change datatype' is set for what yo want

For example if the 'FASTQ Quality Trimmer' will accept the files change the settings so that there will never be any trimming.

Just an idea.

If this will not work I suspect you will have to upload them again. Cheers Guy

ADD COMMENTlink modified 10 months ago • written 10 months ago by Guy Reeves1.0k
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