Hi all
We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot 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 **************************************************************************
Hi all,
An old question without reply. Is there a solution to this problem ? Thanks for your help.
nico
Le 18/07/2014 12:51, Ulf Schaefer a écrit :
Hi all
We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot 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/
I don't think there is a way given the implementation. The name of the association is repeatname_0|input1 but the | is treated as a special symbol so it won't be used to get the parameter.
I have opened a PR to allow this:
https://github.com/galaxyproject/galaxy/pull/662
The syntax in the above example would be something like #{repeatname_0.input1 | basename}.bam after that pull request.
-John
On Tue, Jul 28, 2015 at 2:47 PM, Nicolas Lapalu nicolas.lapalu@versailles.inra.fr wrote:
Hi all,
An old question without reply. Is there a solution to this problem ? Thanks for your help.
nico
Le 18/07/2014 12:51, Ulf Schaefer a écrit :
Hi all
We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot 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/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
John Chilton -
Nicolas Lapalu -
Ulf Schaefer