Opened 9 years ago
Closed 9 years ago
#834 closed task (fixed)
Auto-analyze when sequencing has ended
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | critical | Milestone: | Reggie v4.1 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description
Reggie should be able to automatically detect when a sequencing run has ended and, after making some checks, start the demux step and other downstream secondary analysis.
The "Register sequencing started" wizard should have an option to enable the automatic analysis. It should be something that is similar to the "auto-confirm" option in the "Start demux" wizard.
Implementation details:
- When the auto-analyze option is enabled the
SequencingRun
item is connected with aJob
(external). - A signal handler is used for status updates. We need to implement a new handler that is similar to the Open Grid Scheduler handler.
- The signal handler will check the
<run-archive>
for certain files and update the job status based on which files that are present:- no files found --> WAITING
- Data folder found --> EXECUTING (clustering)
RunParameters.xml
--> EXECUTING (sequencing)RunCompletionStatus.xml
--> DONE- (more investigations may be needed)
- When the sequencing has completed it should import data from the files just as if the "Register sequencing ended" wizard had been used.
- It should always be possible to run the "Register sequencing ended" wizard manually.
- The auto-confirmation service will then take over and detect the ended job. It should run either
picard
or thegenseq_check_illumina_dir.pl
program for a preliminary check. - If all seems to be ok, the demux step should be started using the default options (including auto-confirm=true).
Change History (13)
comment:1 by , 9 years ago
Milestone: | Reggie v4.x → Reggie v4.1 |
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Status: | new → assigned |
comment:2 by , 9 years ago
comment:3 by , 9 years ago
(In [3692]) References #834: Auto-analyze when sequencing has ended
Sequencing runs with "auto-analyze" enabled are now saved with a job item linked to them. Signal processing is not implemented so the job will just sit in "waiting" status.
The "Register sequencing ended" wizard now display a warning if trying to maually register a sequencing run with "auto-analyze" as ended.
comment:4 by , 9 years ago
(In [3697]) References #834: Auto-analyze when sequencing has ended
Implemented progress reporting for sequencing jobs. The signal handler implementation now accepts a flow cell barcode. The status checking has been refactored to make it possible to call different scripts for different type of jobs. The NextSeqJobStatusReuqest
uses a new pipeline script nextseq_status.sh
that check which files and folders for a given flow cell that exists in the run archive.
comment:5 by , 9 years ago
(In [3699]) References #834: Auto-analyze when sequencing has ended
Implemented job completion handler for sequencing runs. The completion handler will download the RunParameters.xml
and extract the same information as the "Register sequencing ended" wizard. After the completion handler has ended the sequencing run should end up in the "Confirm sequencing completed" wizard.
comment:6 by , 9 years ago
(In [3700]) References #834: Auto-analyze when sequencing has ended
Started to implement SequencingRunAutoConfirmer
. It will currently accept and confirm sequencing runs that has ended with Job.Status=DONE. Checking with Picard is not yet implemented.
Starting the demux step is also not implmented so the sequencing run will end up in "Start demux" wizard.
comment:7 by , 9 years ago
comment:8 by , 9 years ago
(In [3714]) References #834: Auto-analyze when sequencing has ended
Re-factored the code for submitting demux jobs to the cluster. More or less everything is in place, except that the barcode files needed by Picard are not genered. This is due to the auto-confirmation needs to work in a single transaction, but the current barcode files exporter require the data to committed first.
comment:9 by , 9 years ago
comment:10 by , 9 years ago
(In [3716]) References #834: Auto-analyze when sequencing has ended
The barcode files exporter for the picard demux step has been fixed so that it works with uncommitted items. The demux step should now be working again and the auto-confirm functionality is fully implemented. It only remains to clean up the code and make some final tests.
comment:11 by , 9 years ago
comment:12 by , 9 years ago
(In [3718]) References #834: Auto-analyze when sequencing has ended
The "Register sequencing ended" wizard now display some more information about sequencing runs that have auto-analyze enabled. It is still possible to manually register the sequencing as ended (and disabled auto-analyze) but a warning is displayed.
comment:13 by , 9 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
(In [3691]) References #834: Auto-analyze when sequencing has ended
Added "auto-analyze" option to the "Register sequencing started" wizard. When enabled, a cluster from the configuration file should be selected. It is also possible to select job priority and debug mode (eg. the same parameters as in the "Start demux" wizard).
The parameters are currently ignored by the registration.