update release notes for 0.9.9.8

ReleaseNotes.txt

@@ -1,3 +1,100 @@
+=========== Changes for Bpipe Version 0.9.9.8 ============
+
+
+   - Feature: options statement for easy parsing of script specific
+     command line arguments 
+
+   - Add workaround to fix possible failure on old pipelines checking 
+     file existence 
+
+   - BUG: Fix spurious error printed if broken symbolic link present 
+
+   - BUG: prevent agent launched commands hanging due to if bpipe prompts 
+     for information
+
+   - Feature: add fileSystemSyncTimeMs which allows for customizable delay in 
+     file system sync before failing pipeline on missing output 
+
+   - BUG: fix regression - transform using regex does not substitute groups
+
+     eg: transform('(.*)_R1.fastq') to("\$1.txt") { ...  } 
+
+   - Many fixes / optimisations to GCloud usage: 
+     - make workingDirectory specified for stage automatically
+       placed within mounted storage 
+
+     - inherit region from main config inside
+       filesystems, so it does not need to be double specified
+
+     - support preemptible flag passed to google cloud
+       instances 
+
+     - add sha1 hash of pipeline path / host to
+       instanceid to make it unique b/w pipelines 
+
+     - fix region configured
+       for cloud executor overriding region specified with -L 
+
+     - search for root input files in all filesystems, not only
+         those configured as storages for stages 
+
+     - fix zone flag missing from gcloud commands, don't
+       die mounting storage if instance not created 
+
+     - support using split / partitioned regions in cloud provider storage 
+
+   - BUG: Don't start executor pools when user is only testing the pipeline 
+
+   - BUG: ensure that executors clean up even if they error in stop
+     command 
+
+   - Fix table output format so it shows correctly in GitHub markdown 
+
+   - Better behavior for bpipe test with send, and send for missing outputs 
+
+   - BUG: input patterns with dir in the pattern causing error / exception 
+
+   - Feature: support for reply -to in JMS bpipe agent 
+
+     If the reply-to or JMSReplyTo header is set, the bpipe agent will now 
+     send a message containing the original command and pipeline success / fail 
+     to specified reply-to address (allows eg: camel inOut routing)
+
+   - BUG: Fix inverted logic causing incorrect detection of file existence 
+     when file is out of sync, causing file systems with high latency 
+     to fail sporadically
+
+   - Better tolerance of file system sync issues for files referenced 
+     using file(...) 
+
+   - BUG: `from` sometimes failing to ensure specified input is resolved in
+     preference to other available inputs preceding it in the
+     pipeline 
+
+   - BUG: from sometimes selecting incorrect input in complex scenarios 
+
+   - BUG: fix file system watchers still created even if poller watcher specified,
+     hence still resulting in file watcher exhaustion errors
+
+   - BUG: -d option not respected in some situations, incorrect output dir may
+     be used if default output already referenced 
+
+   - Feature: Support for Groovy 2.5.6 via optional gradle.properties setting
+
+   - Feature: support for template dirs created by bpipe agent with incrementing 
+     values. Directories containing {inc} will be named with auto-incrementing
+     counter.
+
+   - Feature: 'terminateOnError' flag in send attributes causes 
+     notification failure as to be treated as error 
+
+   - BUG: improve unfriendly / incorrect behavior when duplicate mappings exist in transform 
+
+   - BUG: checks sometimes re-executing when not necessary 
+
+   - Feature: `bpipe touch` command updates files from current run 
+     of pipeline to new timestamps so they do not re-run on `bpipe run`.
+
 =========== Changes for Bpipe Version 0.9.9.7 ============
 
    - Fix incorrect "abnormal termination" messages