20b38b38f3
Updated from SnakeYAML 1.6 to 1.7.
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Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:47:49 +00:00
6dec042288
Re-enabling indel cleaning, explicitly calling fix mates in the case where indel cleaning is not scatter/gathered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4324 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 20:37:49 +00:00
b24172c80f
Queue now utilizes .[file].done to allow skipping of previous jobs, if they have been completed. This is, unfortunately, reliant on a python script to do the post-execution touching of .done files.
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That is to say, proper resumability is live (but not extensively tested)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4312 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 00:16:53 +00:00
6f6d2eb31f
Told people this worked...forgot to commit!
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-c
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4306 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 03:46:00 +00:00
c1720cc8f5
Now compiles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4295 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 18:49:53 +00:00
c581bd2d84
Minor modifications to fCP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4294 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 18:29:24 +00:00
fd5970fdd4
At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.
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No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 21:30:48 +00:00
5e710050d6
minor change, bamFiles comes from the input list, not the script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4170 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:03:35 +00:00
1a14dbee1e
Adding in .bam indexing; commit for Khalid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4169 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 15:21:41 +00:00
2ffa98aea5
Ugh! varout --> out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4157 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 02:34:41 +00:00
d7edce31a2
Commit of fCP for Khalid
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4156 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 02:24:25 +00:00
576ae30df1
A version of the full calling pipeline queue script that fully compiles without String/File/NamedFile type exceptions (e.g. expected String but got NamedFile/Expected NamedFile but got File). Pipeline itself is under testing with 5 bam files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4154 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-28 22:51:11 +00:00
c6441b585a
Actually hook up the new indel genotyper and merge analyses into DAG (aka "i forgot to add()")
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4149 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 18:00:50 +00:00
7908237b90
Full calling pipeline now calls indels through the indel genotyper, merges with combine variants, and filters on them. Since new genomic annotator is fast, it is no longer scatter-gathered.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4144 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 16:28:24 +00:00
6eb1559c1d
End-to-end calling works again (changes to walker arguments, and changes to queue, affect its validity, so it often goes out-of-date before I try to use it again)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4116 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 18:52:44 +00:00
0028b884d8
Reformatting and tweaks to the end-to-end pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4066 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 20:29:48 +00:00
3a4977c75e
Re-add the 1KG trigger as a comp as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4045 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-16 18:19:47 +00:00
4f51a02dea
Changed logging level to default at INFO instead of WARN.
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Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 16:42:48 +00:00
5815348ebc
Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3941 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 20:05:27 +00:00
9132c98eec
Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 22:04:02 +00:00
54d93f63d2
Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 21:35:50 +00:00
0f9baa2e94
Ha ha ha ha ha
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:(
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3902 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 20:48:35 +00:00
7a5ee485d2
Full pipeline now works through DAG creation. First draft; more work to do to make it cleaner and better command-line input handling (and properties handling); but the DAG is rendered and looks good.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3898 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 19:36:17 +00:00
4d4cf6e1dc
Updates to calling pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 18:37:20 +00:00
62a9217a61
A brute-force exome/genome independent end-to-end cleaning/calling pipeline using Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3894 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-29 13:17:14 +00:00
kshakir
chartl