Update genotype2develop #45
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added 12 commits
July 18, 2019 16:50
…ndels into updateGenotype2develop
…olders for terra version for JointGenotyping workflow
…tk4-germline-snps-indels into updateGenotype2develop
bshifaw
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Jan 13, 2020
* Updated to gatk4.1, Update VariantRecal syntax * added samtools path variable * Updated wording * add a version of joint-discovery that takes in an array for gvcfs * Update README.md * increased mem for SNPsVariantRecalibrator for papiv2 * increased mem for SNPsVariantRecalibrator for papiv2 * increased memory to run on papiv2 * correction to variable names in json * corrected parameter syntax for SNPsVariantRecalibrator task * Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller # * Added WDL 1.0 version of JointGenotyping to soon replace joint discovery wdl * Update genotype2develop (#44) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * Update genotype2develop (#45) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#46) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#48) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * added recent updates from dsde-pipelines repo to terra version * removed unnecessary optional override variables * replaced '$' with '~' * updated broad reference bucket path * Add important notes regarding JointGenotype workflow to Readme * minor update to Readme, renamed input file name in json * minor spelling * Added allele-specific annotations to HC command * Updated import url to the next release tag
bshifaw
pushed a commit
that referenced
this pull request
Feb 24, 2020
* Updated to gatk4.1, Update VariantRecal syntax * added samtools path variable * Updated wording * add a version of joint-discovery that takes in an array for gvcfs * Update README.md * increased mem for SNPsVariantRecalibrator for papiv2 * increased mem for SNPsVariantRecalibrator for papiv2 * increased memory to run on papiv2 * correction to variable names in json * corrected parameter syntax for SNPsVariantRecalibrator task * Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller # * Added WDL 1.0 version of JointGenotyping to soon replace joint discovery wdl * Update genotype2develop (#44) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * Update genotype2develop (#45) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#46) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#48) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * added recent updates from dsde-pipelines repo to terra version * removed unnecessary optional override variables * replaced '$' with '~' * updated broad reference bucket path * Add important notes regarding JointGenotype workflow to Readme * minor update to Readme, renamed input file name in json * minor spelling * Added allele-specific annotations to HC command * Updated import url to the next release tag * correction to location of JointGenotyping input path location * Added note regarding Reblocking GVCFS for GnarlyGenotyper
bshifaw
pushed a commit
that referenced
this pull request
Mar 6, 2020
* Updated to gatk4.1, Update VariantRecal syntax * added samtools path variable * Updated wording * add a version of joint-discovery that takes in an array for gvcfs * Update README.md * increased mem for SNPsVariantRecalibrator for papiv2 * increased mem for SNPsVariantRecalibrator for papiv2 * increased memory to run on papiv2 * correction to variable names in json * corrected parameter syntax for SNPsVariantRecalibrator task * Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller # * Added WDL 1.0 version of JointGenotyping to soon replace joint discovery wdl * Update genotype2develop (#44) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * Update genotype2develop (#45) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#46) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * Update genotype2develop (#48) * added updated joint-discovery wdl, needs testing * Added place holder for terra verion of JointGenotyping wdl * Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow * updated the terra version of the JointGenotyping * added urls for imports for JointGenotyping workflows * Updated ReadMe * added missing runtime variables * added missing runtime variable * added recent updates from dsde-pipelines repo to terra version * removed unnecessary optional override variables * replaced '$' with '~' * updated broad reference bucket path * Add important notes regarding JointGenotype workflow to Readme * minor update to Readme, renamed input file name in json * minor spelling * Added allele-specific annotations to HC command * Updated import url to the next release tag * correction to location of JointGenotyping input path location * Added note regarding Reblocking GVCFS for GnarlyGenotyper * Updated contact us message
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added missing runtime variables