You cannot directly couple different workflows.

But you could indeed copy all outputs of the different workflows into one history, and create a separate workflow with your tool to work on all those input files.


Cheers,
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 02/12/2013 04:31 PM, Hagai Cohen wrote:

Thanks for your answer.
I figured that there is an option to run a workflow on multiple files, but I can't merge the outputs afterwardsl. I would like the workflow to return one final output.

But you gave me another idea.
Can I somehow tell one workflow to run on other workflow output?
If this can be done, I can run 100 different workflows with bowtie & statistics, each working on one fastq file, than run another workflow which gets 100 xls inputs and merge them to one.




On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| <joachim.ja...@vib.be <mailto:joachim.ja...@vib.be>> wrote:

    Hi Hagai,

    Actually, using a workflow, you are able to select multiple input
    files, and let the workflow run separately on all input files.

    I would proceed by creating a data library for all your fastq
    files, which you can upload via FTP, or via a system directory.
    You can use a sample of your fastq files to create the steps in a
    history you want to perform, and extract a workflow out of it.
    Next, copy all fastq files from a data library in a new history,
    and run your workflow on the all input files.

    I hope this helps you further,
    Joachim


    Joachim Jacob

    Rijvisschestraat 120, 9052 Zwijnaarde
    Tel: +32 9 244.66.34 <tel:%2B32%209%20244.66.34>
    Bioinformatics Training and Services (BITS)
    http://www.bits.vib.be
    @bitsatvib


    On 02/12/2013 04:02 PM, Hagai Cohen wrote:

        Hi,
        I'm looking for a preferred way of running Bowtie (or any
        other tool) on multiple input files and run statistics on the
        Bowtie output afterwards.

        The input is a directory of files fastq1..fastq100
        The bowtie output should be bed1...bed100
        The statistics tool should run on bed1...bed100 and return
        xls1..xls100
        Then I will write a tool which will get xls1..xls100 and merge
        them to one final output.

        I searched for a smiliar cases, and I couldn't figure anyone
        which had this problem before.
        Can't use the parallelism tag, because what will be the input
        for each tool? it should be a fastq file not a directory of
        fastq files.
        Neither I would like to run each fastq file in a different
        workflow - creating a mess.

        I thought only on two solutions:
        1. Implement new datatypes: bed_dir & fastq_dir and implements
        new tool wrappers which will get a folder instead of a file.
        2. merge the input files before sending to bowtie, and use
        parallelism tag to make them be splitted & merged again on
        each tool.

        Does anyone has any better suggestion?

        Thanks,
        Hagai











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