update workflow versions in docs (#1145)

website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md

@@ -7,7 +7,7 @@ slug: /Pipelines/Exome_Germline_Single_Sample_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [ExomeGermlineSingleSample_v3.1.15](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
+| [ExomeGermlineSingleSample_v3.1.16](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
 
 
 The Exome Germline Single Sample pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md

@@ -7,7 +7,7 @@ slug: /Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [UltimaGenomicsWholeGenomeGermline_v1.0.0](https://github.com/broadinstitute/warp/releases) | June, 2022 | [Elizabeth Kiernan](mailto:[email protected]) & [Kaylee Mathews](mailto:[email protected])| Please file GitHub issues in warp or contact [the wARP team](mailto:[email protected]) |
+| [UltimaGenomicsWholeGenomeGermline_v1.0.13](https://github.com/broadinstitute/warp/releases) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) & [Kaylee Mathews](mailto:[email protected])| Please file GitHub issues in warp or contact [the wARP team](mailto:[email protected]) |
 
 ![UG_diagram](ug_diagram.png)
 
@@ -19,7 +19,7 @@ The [Ultima Genomics Whole Genome Germline (UG_WGS) workflow](https://github.com
 
 Ultima Genomics sequencing is a novel technology that produces single-read, flow-based data ([Almogy et al., 2022](https://www.biorxiv.org/content/10.1101/2022.05.29.493900v1)). The sequencing platform works by flowing one nucleotide at a time in order, iteratively. This is in contrast to traditional technologies that do all four nucleotides at once. This iterative approach ensures that only one dNTP is responsible for the signal and it does not require the blocking of dNTPs.  
 
-### What does the workflow do? 
+### What does the workflow do?
 
 The workflow requires either an aligned CRAM output of the sequencing platform or an unmapped BAM as input. Overall, it aligns reads to a reference genome, marks duplicate reads, calls variants, post-processes variants in the output VCF in preparation for joint calling, and calculates quality control metrics. The workflow outputs a (re)aligned CRAM, an annotated GVCF with index, and quality metrics. 
 
@@ -201,7 +201,7 @@ The workflow implements initial variant calling with a version of HaplotypeCalle
 | [Utilities.ScatterIntervalList](https://github.com/broadinstitute/warp/blob/develop/tasks/broad/Utilities.wdl) | IntervalListTools | Picard | Splits the calling interval list into sub-intervals in order to perform variant calling on the sub-intervals. |
 | [Tasks.HaplotypeCaller](https://github.com/broadinstitute/warp/blob/develop/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl) | HaplotypeCaller | GATK | Performs initial variant calling on the aligned BAM file and outputs sub-interval GVCFs and a bamout file. |
 
-### 6. Merge VCFs and BAMs and convert GVCF to VCF 
+### 6. Merge VCFs and BAMs and convert GVCF to VCF
 The workflow performs multiple post-processing steps to prepare the VCF for downstream joint calling. The HaplotypeCaller GVCF outputs are merged into a single GVCF and then converted to VCF in preparation for this post-processing.
 
 | Task name and WDL link | Tool | Software | Description | 

website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md

@@ -7,7 +7,7 @@ slug: /Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| WholeGenomeGermlineSingleSample_v3.1.14 (see [releases page](https://github.com/broadinstitute/warp/releases)) | August, 2022 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
+| WholeGenomeGermlineSingleSample_v3.1.17 (see [releases page](https://github.com/broadinstitute/warp/releases)) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
 
 ## Introduction to the Whole Genome Germline Single Sample Pipeline
 The Whole Genome Germline Single Sample (WGS) pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human whole-genome sequencing data. It includes the DRAGEN-GATK mode, which makes the pipeline functionally equivalent to DRAGEN’s analysis pipeline (read more in this [DRAGEN-GATK blog](https://gatk.broadinstitute.org/hc/en-us/articles/360039984151)).

website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/wgs.methods.md

@@ -2,13 +2,13 @@
 sidebar_position: 2
 ---
 
-# Whole Genome Germline Single Sample v3.1.6 Methods (Default workflow)
+# Whole Genome Germline Single Sample v3.1.17 Methods (Default workflow)
 
 The following contains a detailed methods description outlining the pipeline’s process, software, and tools that can be modified for a publication methods section.
 
 ## Detailed methods for the default Whole Genome Germline Single Sample workflow
 
-Preprocessing and variant calling was performed using the WholeGenomeGermlineSingleSample v3.1.6 pipeline using Picard v2.26.10, GATK v4.2.6.1, and Samtools v1.11 with default tool parameters unless otherwise specified. All reference files are available in the public [Broad References Google Bucket](https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0). The pipeline follows GATK Best Practices as previously described ([Van der Auwera & O'Connor, 2020](https://www.oreilly.com/library/view/genomics-in-the/9781491975183/)) as well as the Functional Equivalence specification ([Regier et al., 2018](https://www.nature.com/articles/s41467-018-06159-4)).
+Preprocessing and variant calling was performed using the WholeGenomeGermlineSingleSample v3.1.17 pipeline using Picard v2.26.10, GATK v4.3.0.0, and Samtools v1.11 with default tool parameters unless otherwise specified. All reference files are available in the public [Broad References Google Bucket](https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0). The pipeline follows GATK Best Practices as previously described ([Van der Auwera & O'Connor, 2020](https://www.oreilly.com/library/view/genomics-in-the/9781491975183/)) as well as the Functional Equivalence specification ([Regier et al., 2018](https://www.nature.com/articles/s41467-018-06159-4)).
 
 ### Pre-processing and quality control metrics
 
@@ -34,7 +34,7 @@ The pipeline’s final outputs included metrics, validation reports, an aligned
 
 ## Detailed methods for the Functional Equivalence mode of the Whole Genome Germline Single Sample workflow
 
-Preprocessing and variant calling was performed using the WholeGenomeGermlineSingleSample v3.1.6 pipeline using v2.26.10, GATK v4.2.6.1, and Samtools v1.11 with default tool parameters unless otherwise specified. All reference files are available in the public [Broad References Google Bucket](https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0). The pipeline is functionally equivalent (as described in GATK Support: https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915) to DRAGEN v3.4.12. 
+Preprocessing and variant calling was performed using the WholeGenomeGermlineSingleSample v3.1.17 pipeline using v2.26.10, GATK v4.3.0.0, and Samtools v1.11 with default tool parameters unless otherwise specified. All reference files are available in the public [Broad References Google Bucket](https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0). The pipeline is functionally equivalent (as described in GATK Support: https://gatk.broadinstitute.org/hc/en-us/articles/4410456501915) to DRAGEN v3.4.12. 
 
 ### Pre-processing and quality control metrics
 
@@ -57,6 +57,7 @@ Prior to variant calling, the DRAGEN STR model was calibrated using the Calibrat
 The pipeline’s final outputs included metrics, validation reports, an aligned CRAM with index, and a reblocked GVCF containing variant calls with an accompanying index.
 
 ## Previous methods documents
+- [WholeGenomeGermlineSingleSample_v3.1.6](https://github.com/broadinstitute/warp/blob/WholeGenomeGermlineSingleSample_v3.1.8/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/wgs.methods.md)
 - [WholeGenomeGermlineSingleSample_v3.0.0](https://github.com/broadinstitute/warp/blob/WholeGenomeGermlineSingleSample_v3.0.0/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/wgs.methods.md)
 - [WholeGenomeGermlineSingleSample_v2.5.0](https://github.com/broadinstitute/warp/blob/WholeGenomeGermlineSingleSample_v2.5.0/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/wgs.methods.md)
 - [WholeGenomeGermlineSingleSample_v2.3.7](https://github.com/broadinstitute/warp/blob/WholeGenomeGermlineSingleSample_v2.3.7/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/wgs.methods.md)