Changing datatype of multiple datasets in batch

Question: Changing datatype of multiple datasets in batch

18 months ago by

Canada

ropolocan • 30 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 • 600 views

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modified 18 months ago by Guy Reeves • 1.0k • written 18 months ago by ropolocan • 30

18 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link modified 18 months ago • written 18 months ago by ropolocan • 30

18 months ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k 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 COMMENT • link modified 18 months ago • written 18 months ago by Guy Reeves • 1.0k

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