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: >> 1. make a history, doing the steps you want to do on one input file >> 2. create a workflow of that history >> 3. assemble all input files in one history >> 4. 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 >>> >>> ************************************************************************** >>> >>> The information contained in the EMail and any attachments is >>> confidential and intended solely and for the attention and use of the >>> named addressee(s). It may not be disclosed to any other person >>> without the express authority of Public Health England, or the >>> intended recipient, or both. If you are not the intended recipient, >>> you must not disclose, copy, distribute or retain this message or any >>> part of it. This footnote also confirms that this EMail has been >>> swept for computer viruses by Symantec.Cloud, but please re-sweep any >>> attachments before opening or saving. http://www.gov.uk/PHE >>> ************************************************************************** >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>> >> > ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ************************************************************************** ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
