update reference

Author: denis-yuen

docs/advanced-topics/batch-services.rst

@@ -71,7 +71,7 @@ Usage
 
    ::
 
-       consonance run --tool-dockstore-id quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 --run-descriptor Dockstore.json --flavour <AWS instance-type>
+       consonance run --tool-dockstore-id quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 --run-descriptor Dockstore.json --flavour <AWS instance-type>
 
 .. discourse::
        :topic_identifier: 1545

docs/advanced-topics/best-practices/wdl-best-practices.rst

@@ -38,7 +38,7 @@ This example includes author, email, and description metadata:
         }
 
         runtime {
-            docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0"
+            docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
             memory: mem_gb + "GB"
         }
 

docs/advanced-topics/legacy/legacy-getting-started-with-cwl.rst

@@ -307,7 +307,7 @@ the JSON config file:
            --rm \
            --env=TMPDIR=/tmp \
            --env=HOME=/var/spool/cwl \
-           quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 \
+           quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 \
            bash \
            /usr/local/bin/bamstats \
            4 \

docs/faq.rst

@@ -324,7 +324,7 @@ on the underlying host and the temporary directory at
         --rm \
         --env=TMPDIR=/tmp \
         --env=HOME=/var/spool/cwl \
-        quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 \
+        quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 \
         bash \
         /usr/local/bin/bamstats \
         4 \

docs/getting-started/getting-started-with-cwl.rst

@@ -302,7 +302,7 @@ the JSON config file:
            --rm \
            --env=TMPDIR=/tmp \
            --env=HOME=/var/spool/cwl \
-           quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 \
+           quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 \
            bash \
            /usr/local/bin/bamstats \
            4 \

docs/getting-started/getting-started-with-nextflow.rst

@@ -46,7 +46,7 @@ information and settings within scopes, such as manifest and docker.
         mem_gb = '4'
     }
 
-    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0'
+    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-7'
     docker {
         enabled = true
         docker.runOptions = '-u $(id -u):$(id -g)'
@@ -86,7 +86,7 @@ syntax for setting values within a scope.
 
 ::
 
-    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0'
+    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-7'
 
 The last scope of the file is the docker scope. This scope does not
 define the container that we use, instead it defined other Docker
@@ -216,7 +216,7 @@ with the new file.
         mem_gb = '4'
     }
 
-    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0'
+    process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-7'
     docker {
         enabled = true
         docker.runOptions = '-u $(id -u):$(id -g)'

docs/getting-started/getting-started-with-wdl.rst

@@ -75,7 +75,7 @@ repository:
         }
 
         runtime {
-            docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0"
+            docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
             memory: mem_gb + "GB"
         }
     }
@@ -229,7 +229,7 @@ allocated for the task, but we will keep it simple for now.
 ::
 
     runtime {
-        docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0"
+        docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
         memory: mem_gb + "GB"
     }
 

docs/launch-with/launch.rst

@@ -49,7 +49,7 @@ follows:
 ::
 
     # make a runtime JSON template and fill in desired inputs, outputs, and other parameters
-    $ dockstore tool convert entry2json --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 > Dockstore.json
+    $ dockstore tool convert entry2json --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 > Dockstore.json
     $ vim Dockstore.json
     # note that the empty JSON config file has been filled with an input file retrieved via http
     $ cat Dockstore.json
@@ -66,7 +66,7 @@ follows:
       }
     }
     # run it locally with the Dockstore CLI
-    $ dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0 --json Dockstore.json
+    $ dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 --json Dockstore.json
 
 This information is also provided in the "Launch With" section of every
 tool.