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updated readme

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1 parent 13f93da commit 44d16017c34bb3563e5a170e926a8943c6c51e2f @fstrozzi committed Sep 24, 2012
Showing with 6 additions and 3 deletions.
  1. +6 −3 README.md
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@@ -52,9 +52,6 @@ For each job, BioGrid will set an output name according to a UUID generated on t
```
IMPORTANT: the UUID will be the same for all the jobs submitted in a same BioGrid run, the only changing part will be the incremental number.
-**If no extension is specified for the ```<output>``` placeholder in the command line definition, BioGrid will assume the job will generate more than one output file and that those files will be saved into the folder specified by the "-o" option**. Therefore it will manage the output as a whole directory, copying and/or removing the entire folder if ```-r``` and ```-e``` options are present (check the [Other options](https://github.com/fstrozzi/bioruby-grid#other-options) section to see what these options are expected to do).
-The same rule for output name apply also in the case of an output folder.
-
If you want to do some [Advanced stuff](https://github.com/fstrozzi/bioruby-grid#advanced-stuff) and run parameters testing, the output names will be changed accordingly by BioGrid. So if I am running BioGrid to test some parameter ```-L``` for my favorite tool, and I am sampling it, with three different values, let's say 3, 7 and 10 the corresponding output files will be:
```shell
@@ -70,6 +67,12 @@ If you are using the ```--param``` options to test non-numerical parameters, the
9ec55d90_tophat_001-param:--fast.sam
```
+###Differences between output files and output folder
+
+BioGrid will act differently if the output of a single job is a file or a folder. You need to specify this, by adding a file extension to the ```<output>``` placeholder. So, for instance, if the output file of my job is a BAM file, I will need to specify this in the command line definition, by putting a ```<output>.bam``` .
+**If no extension is specified for the ```<output>``` placeholder in the command line definition, BioGrid will assume the job will generate more than one output file and that those files will be saved into the folder specified by the "-o" option**. Therefore it will manage the output as a whole directory, copying and/or removing the entire folder if ```-r``` and ```-e``` options are present (check the [Other options](https://github.com/fstrozzi/bioruby-grid#other-options) section to see what these options are expected to do).
+
+The naming conventions for the output folder are same as for the output files.
Other options
-------------

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