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
@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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