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
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
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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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