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briandoconnorbriandoconnor
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Merge branch 'release/1.0.8'
2 parents 57dab14 + cc0c40e commit 48cd69a

9 files changed

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‎CHANGELOG.md‎

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# 1.0.6
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# 1.0.8
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* SeqWare-CGP-SomaticCore artefact updated to 1.3.1 to handle readgroup count >115 when combining tumour and normal in SNV caller.
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* As part of above updated cgpCaVEManPostProcessing, cgpCaVEManWrapper.
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# 1.0.7
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Todo:
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* SeqWare-CGP-SomaticCore artefact updated to 1.3.0 to handle very long RG ID fields in BAM headers.
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* need to add a new param that passes the URL for metadata even when working in full offline mode, this is a workaround for Romina so she can generate valid XML while using local files -- DONE
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* check to see if I expose timeouts in the conf file -- DONE, Solomon to review
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* patch in at least packageResults.pl to force SM field in BAM headers to lower case? -- WON'T FIX
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* get corrected version of Keiran's tools that properly handle threading -- DONE
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# 1.0.6
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* added a new param that passes the URL for metadata even when working in full offline mode, this is a workaround for Romina so she can generate valid XML while using local files
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* expose timeouts in the conf file
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* corrected version of Keiran's tools that properly handle threading
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* Changes to core Sanger packages to fix error in limit based processing
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* ArtifactId: SeqWare-CGP-SomaticCore_opt
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* Version: 1.2.3
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* updated version of Adam's GNOS wrappers that correctly timeout on a 0% upload GNOS connection... this new version of the code doesn't use perl threading which can be unreliable. Also need to take this as an opportunity to make artifacts -- Solomon TODO
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* an S3 mode where XML/BAMs are read from S3 URLs and the results written back to S3... we have the latter but the former needs to be done -- DONE
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* eliminate the use of the forked pcap script since Keiran accepted the local file fix the artifact below didn't include a needed change to xml_to_bas.pl to support local file mode -- DONE
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* Kyle reported and error on cleanup: "Can't delete folder: /datastore/oozie-e706677a-b7ff-4905-90f2-c717ce2622bf/./temp-62eb639e-cf9f-48cf-a2d3-d0ab996aac05" -- FIXED, I believe this was fixed in 1.0.5.1 hotfix, waiting for more info from Kyle
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* updated version of Adam's GNOS wrappers that correctly timeout on a 0% upload GNOS connection... this new version of the code doesn't use perl threading which can be unreliable.
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* an S3 mode where results are written back to S3
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* eliminated the use of the forked pcap script since Keiran accepted the local file fix the artifact below didn't include a needed change to xml_to_bas.pl to support local file mode
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# 1.0.5.1 Hotfix
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‎README.md‎

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Email Brian if you have questions.
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* Keiran Raine
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* Keiran Raine <kr2@sanger.ac.uk>
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* Brian O'Connor <boconnor@oicr.on.ca>
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## Environment Requirements
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* [cgpVcf v1.2.2](https://github.com/cancerit/cgpVcf/archive/v1.2.2.tar.gz)
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* [alleleCount v1.2.1](https://github.com/cancerit/alleleCount/archive/v1.2.1.tar.gz)
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* [cgpBinCounts v1.0.2](https://github.com/cancerit/cgpBinCounts/archive/v1.0.2.tar.gz)
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* [cgpNgsQc v1.0.2](https://github.com/cancerit/cgpNgsQc/archive/v1.0.3.tar.gz)
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* [cgpNgsQc v1.0.3](https://github.com/cancerit/cgpNgsQc/archive/v1.0.3.tar.gz)
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* [ascatNgs v1.5.1](https://github.com/cancerit/ascatNgs/archive/v1.5.1.tar.gz)
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* [cgpPindel v1.3.2](https://github.com/cancerit/cgpPindel/archive/v1.2.0.tar.gz)
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* [cgpCaVEManPostProcessing v1.2.0](https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.2.0.tar.gz)
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* [cgpCaVEManWrapper v1.5.1](https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.5.1.tar.gz)
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* [cgpPindel v1.3.2](https://github.com/cancerit/cgpPindel/archive/v1.3.2.tar.gz)
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* [cgpCaVEManPostProcessing v1.3.0](https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.3.0.tar.gz)
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* [cgpCaVEManWrapper v1.7.2](https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.7.2.tar.gz)
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* [BRASS v2.2.0](https://github.com/cancerit/BRASS/archive/v2.2.0.tar.gz)
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* [VAGrENT v2.0.0](https://github.com/cancerit/VAGrENT/archive/v2.0.0.tar.gz)
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* [grass v1.0.1](https://github.com/cancerit/grass/archive/v1.0.1.tar.gz)

‎pom.xml‎

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<!-- MAKE SURE YOU UPDATE THE workflow.properties FILE TOO -->
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<artifactId>SangerPancancerCgpCnIndelSnvStr</artifactId>
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<!-- MAKE SURE YOU UPDATE THE workflow.properties FILE TOO -->
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<version>1.0.7</version>
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<version>1.0.8</version>
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<packaging>jar</packaging>
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<!-- MAKE SURE YOU UPDATE THE workflow.properties FILE TOO -->
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<name>SangerPancancerCgpCnIndelSnvStr</name>
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<dependency>
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<groupId>SeqWare-CGP-SomaticCore</groupId>
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<artifactId>SeqWare-CGP-SomaticCore_opt</artifactId>
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<version>1.3.0</version>
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<version>1.3.1</version>
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<type>tar.gz</type>
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</dependency>
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<dependency>

‎workflow.properties‎

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workflow-name=SangerPancancerCgpCnIndelSnvStr
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workflow-short-name-version=svcp_1-0-7
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workflow-version=1.0.7
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workflow-short-name-version=svcp_1-0-8
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workflow-version=1.0.8
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workflow-description=Runs the WTSI CGP Copynumber, Indel, Snv and Structural variation core pipeline.
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workflow-url=https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_SangerPancancerCgpCnIndelSnvStr_1.0.7_SeqWare_1.1.0.zip
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workflow-url=https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_SangerPancancerCgpCnIndelSnvStr_1.0.8_SeqWare_1.1.0.zip
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workflow-src-url=https://github.com/ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore

‎workflow/bin/setup.sh‎

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"https://github.com/cancerit/cgpNgsQc/archive/v1.0.3.tar.gz"
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"https://github.com/cancerit/ascatNgs/archive/v1.5.1.tar.gz"
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"https://github.com/cancerit/cgpPindel/archive/v1.3.2.tar.gz"
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"https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.2.0.tar.gz"
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"https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.5.1.tar.gz"
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"https://github.com/cancerit/cgpCaVEManPostProcessing/archive/v1.3.0.tar.gz"
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"https://github.com/cancerit/cgpCaVEManWrapper/archive/v1.7.2.tar.gz"
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"https://github.com/cancerit/BRASS/archive/v2.2.0.tar.gz"
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"https://github.com/cancerit/VAGrENT/archive/v2.0.0.tar.gz"
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"https://github.com/cancerit/grass/archive/v1.0.1.tar.gz"

workflow/config/CgpCnIndelSnvStrWorkflow.aws.large.ini renamed to workflow/config/ini_examples/CgpCnIndelSnvStrWorkflow.aws.large.ini

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workflow/config/CgpCnIndelSnvStrWorkflow.aws.medium.ini renamed to workflow/config/ini_examples/CgpCnIndelSnvStrWorkflow.aws.medium.ini

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workflow/config/CgpCnIndelSnvStrWorkflow.aws.small.ini renamed to workflow/config/ini_examples/CgpCnIndelSnvStrWorkflow.aws.small.ini

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workflow/config/CgpCnIndelSnvStrWorkflow.bionimbus.ini renamed to workflow/config/ini_examples/CgpCnIndelSnvStrWorkflow.bionimbus.ini

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