CollectSamError_v2.0.0

CollectSamError

CleanUpFailedSubmissions_v2.0.0

CleanUpFailedSubmissions.

BreaKmer_v2.0.0

Initial release of BreaKmer. We are introducing versioning of every TAG pipeline.

Griffin_2.0.0_alpha

Griffin

GATK_CNV_Mutect2_v2.0.0-alpha

GATK_CNV_Mutect2_v2.0.0-alpha
Not fully working yet.

v1.1.2

What's Changed

• Update Mutect2 wdl to Reflect Case and Control Names in the Deliverables by @yueyaog in #19
• GATK4CNV Optional PON Input by @yueyaog in #17
• Add Interval Check Procedure in Duplex Workflow by @yueyaog in #31
• Update CNV and M2 to GATK official workflows by @yueyaog in #38
• Add original HaplotypeCaller wdl from GOTK repo as M2 Subworkflow by @yueyaog in #39
• Clean Up Terra Failed Submissions by @yueyaog in #37
• add extra args for flexible memory allocation for Rsem task in SmartSeq wdl by @stellaning1120 in #42
• Wittyer WDL Output Updates by @yueyaog in #43
• Update CollectSamErrorMetrics.wdl by @lfleming1022 in #41

New Contributors

• @lfleming1022 made their first contribution in #41

Full Changelog: v1.1.1...v1.1.2

v1.1.1

What's Changed

• Griffin Pipeline by @yueyaog in #29
• Downsamplebam by @stellaning1120 in #32
• prevent empty array input by @yueyaog in #33

Full Changelog: v1.0.1...v1.1.1

v1.1.0

What's Changed

• Added validate_wdls.sh by @yueyaog in #22
• Added execution permission of validate_wdl.sh by @yueyaog in #23
• Added the recent PR approved changes from TAG repo by @yueyaog in #24
• Bait set name by @yueyaog in #27
• adding option to fail task by @yueyaog in #28
• Update the input JSON for SvABA by @yueyaog in #25
• Updating M2 to take mem input by @MicahR-Y in #26
• Adding dev version of checkBaitSetName WDL by @MicahR-Y in #30
• BenchmarkCNV wdl by @yueyaog in #16

Full Changelog: v1.0.0...v1.0.1

Intial Release of TAG Workflows

What's Changed

• Benchmark cnv by @yueyaog in #4
• README.md update by @yueyaog in #5
• Benchmark cnv by @yueyaog in #6
• Added GATK4 CNV wdl by @yueyaog in #9
• Gatk cnv m2 by @yueyaog in #10
• Adding LegoPlotter WDL plus gitignore file by @MicahR-Y in #11
• commit of iChor workflow with 2 versions of step1 and 1 version of step2 by @stellaning1120 in #13
• update CNV json and remove old cnv by @yueyaog in #12
• First Commit for Liquid Biopsy Analysis Pipeline by @yueyaog in #14
• BenchmarkCNV: WDL to run wittyer on Trio samples by @yueyaog in #7
• Adding SV WDLs to TAG-public by @MicahR-Y in #18
• Clean up by @yueyaog in #21
• Added Upload plate_qc_metrics Function to SmartSeq QC WDL by @yueyaog in #20

Full Changelog: v0.1.0-alpha...v1.0.0

v0.1.0-alpha

Initial release for ichor.