Update gitter link to arvados/community

[arvados.git] / doc / user / cwl / cwl-runner.html.textile.liquid

diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index ad5d3bd83643e6d9134dbfddddfdf2209be66140..f38cbf1de2334800e223bbca3889644c498fd3d8 100644 (file)
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -25,10 +25,10 @@ h2. Running arvados-cwl-runner
 
 h3. Get the example files
 
-The tutorial files are located in the "documentation section of the Arvados source repository:":https://github.com/curoverse/arvados/tree/master/doc/user/cwl/bwa-mem
+The tutorial files are located in the "documentation section of the Arvados source repository:":https://github.com/arvados/arvados/tree/master/doc/user/cwl/bwa-mem
 
 <notextile>
-<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados</span>
+<pre><code>~$ <span class="userinput">git clone https://github.com/arvados/arvados</span>
 ~$ <span class="userinput">cd arvados/doc/user/cwl/bwa-mem</span>
 </code></pre>
 </notextile>
@@ -69,7 +69,7 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
-        "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+        "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
         "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
         "class": "File",
         "size": 30738986
@@ -82,7 +82,7 @@ h3. Referencing files
 
 When running a workflow on an Arvados cluster, the input files must be stored in Keep.  There are several ways this can happen.
 
-A URI reference to Keep uses the @keep:@ scheme followed by the portable data hash, collection size, and path to the file inside the collection.  For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@.
+A URI reference to Keep uses the @keep:@ scheme followed by either the portable data hash or UUID of the collection and then the location of the file inside the collection.  For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@ or @keep:zzzzz-4zz18-zzzzzzzzzzzzzzz/19.fasta.bwt@.
 
 If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.
 
@@ -100,7 +100,7 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
-        "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+        "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
         "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
         "class": "File",
         "size": 30738986