Dear all
Related to my question yesterday I have another one:
If I run a workflow in batch I can select pairs of files (the old fwd and rev reads fastq files) and the workflow is run however many times, depending on the number of pairs I select.
Unfortunately all other parameters appear to be static, which is not ideal in my case. Specifically I am using bwa the map a large-ish number of (paired) samples to the same reference genome, while simultaneously setting read group information in the resulting sam files. So it's suboptimal to run this with a fixed SM value.
Is there any way of dynamically setting the parameters? The set-at-runtime option also allows for a single parameter value, not a list. Ideally the set-at-runtime option would somehow allow me to input one parameter per file pair.
Thanks very much in advance for your help.
Cheers Ulf
On 01/10/13 14:09, Joachim Jacob | VIB | wrote:
Sorry, my answer doesn't fit your question. :-) J
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote:
Hi Ulf,
What I do:
- make a history, doing the steps you want to do on one input file
- create a workflow of that history
- assemble all input files in one history
- run the workflow and select the multiple input files to run the
workflow on. 5. Optionally: send the results to a new history, for every input file you will get a new history, properly named.
Hope this helps,
Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
On 10/01/2013 02:27 PM, Ulf Schaefer wrote:
Dear all
We frequently find ourselves in situations where a tool needs to be run with a lot of input files. For example, run the GATK UnifiedGenotyper with easily dozens of bam files.
Using the <repeat> in this case requires quite a bit of clicking. Is there a more conventient way fo doing this? Maybe similar to the multi-file-select that is possible for workflow inputs?
I saw some older discussions on this or similar issues, but I am a bit lost what the current official stable proposed solution for this is.
Thanks for your help Ulf
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