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|
> 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 Jacob
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> On 02/12/2013 04:02 PM, Hagai Cohen wrote:
>> 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?
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