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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