KM update WGS pipeline docs

website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md

@@ -6,9 +6,9 @@ sidebar_position: 1
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| WholeGenomeGermlineSingleSample_v3.1.2 (see [releases page](https://github.com/broadinstitute/warp/releases)) | June, 2022 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [Kylee Degatano](mailto:kdegatano@broadinstitute.org) |
+| WholeGenomeGermlineSingleSample_v3.1.6 (see [releases page](https://github.com/broadinstitute/warp/releases)) | August, 2022 | [Elizabeth Kiernan](mailto:ekiernan@broadinstitute.org) | Please file GitHub issues in WARP or contact [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) |
 
-## Introduction to the Whole Genome Germline Single Sample Pipeline 
+## 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)).
 
 
@@ -76,7 +76,7 @@ The latest release of the workflow, example data, and dependencies are available
 ### Input descriptions
 The tables below describe each of the WGS pipeline inputs and reference files. 
 
-Examples of how to specify each input can be found in the example [input configuration files (JSONs)](https://github.com/broadinstitute/warp/tree/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files). 
+Examples of how to specify each input can be found in the example [input configuration files (JSONs)](https://github.com/broadinstitute/warp/tree/master/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files). 
 
 Multiple references are imported as part of a struct from the [DNASeqStruct WDL](https://github.com/broadinstitute/warp/blob/master/structs/dna_seq/DNASeqStructs.wdl), which is located in the WARP [structs library](https://github.com/broadinstitute/warp/tree/master/structs). For references that are part of a struct, the tables below list the relevant struct’s name. 
 
@@ -91,7 +91,7 @@ Overall, the workflow has the following input requirements:
 * Reference genome must be Hg38 with ALT contigs
 
 #### Struct inputs
-The following table describes the inputs imported from a struct. Although these are specified in the WGS workflow using the struct name, the actual inputs for each struct are specified in the [example configuration files](https://github.com/broadinstitute/warp/tree/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files). 
+The following table describes the inputs imported from a struct. Although these are specified in the WGS workflow using the struct name, the actual inputs for each struct are specified in the [example configuration files](https://github.com/broadinstitute/warp/tree/master/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files). 
 
 
 | Input name | Struct name (alias) | Input description | Input type |
@@ -114,7 +114,7 @@ The following table describes the inputs imported from a struct. Although these
 | agg_preemptible_tries |  PapiSettings (papi_settings) | Number of preemtible machine tries for the BamtoCram task. | Int |
 
 #### Additional inputs
-Additional inputs that are not contained in a struct are described in the table below. Similar to the struct inputs, these inputs are specified in the [example configuration files](https://github.com/broadinstitute/warp/tree/develop/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files) or, when noted, are hardcoded into the WDL workflow.
+Additional inputs that are not contained in a struct are described in the table below. Similar to the struct inputs, these inputs are specified in the [example configuration files](https://github.com/broadinstitute/warp/tree/master/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files) or, when noted, are hardcoded into the WDL workflow.
 
 * Optional inputs, like the fingerprint_genotypes_file, need to match your input samples. For example, the fingerprint file in the workflow's [test input configuration JSON](https://github.com/broadinstitute/warp/blob/master/pipelines/broad/dna_seq/germline/single_sample/wgs/input_files/WholeGenomeGermlineSingleSample.inputs.plumbing.masked_reference.json) is set up to check fingerprints for the NA12878 Plumbing sample. The sample name in the VCF matches the name used for the `sample_name` input.
 
@@ -318,7 +318,7 @@ As of November 2021, reblocking is a default task in the WGS pipeline. To skip r
 "WholeGenomeGermlineSingleSample.BamToGvcf.skip_reblocking": true
 ```
 
-The [Reblocking task](https://github.com/broadinstitute/warp/blob/develop/tasks/broad/GermlineVariantDiscovery.wdl) uses the GATK ReblockGVCF tool with the arguments:
+The [Reblocking task](https://github.com/broadinstitute/warp/blob/master/tasks/broad/GermlineVariantDiscovery.wdl) uses the GATK ReblockGVCF tool with the arguments:
 
 ```WDL
 -do-qual-approx -floor-blocks -GQB 20 -GQB 30 -GQB 40 
@@ -371,7 +371,7 @@ The final CRAM files have base quality scores binned according to the [Functiona
 
 
 ## Contact us
-Please help us make our tools better by contacting [Kylee Degatano](mailto:kdegatano@broadinstitute.org) for pipeline-related suggestions or questions.
+Please help us make our tools better by contacting [the WARP team](mailto:warp-pipelines-help@broadinstitute.org) for pipeline-related suggestions or questions.
 
 ## Licensing
 

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

@@ -2,17 +2,17 @@
 sidebar_position: 2
 ---
 
-# Whole Genome Germline Single Sample v3.0.0 Methods (Default workflow)
+# Whole Genome Germline Single Sample v3.1.6 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 3.0.0 pipeline using Picard 2.23.8, GATK 4.2.2.0, and Samtools 1.11 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 v3.1.6 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)).
 
 ### Pre-processing and quality control metrics
 
-Whole genome paired-end reads in unmapped BAM (uBAM) format were first scattered to perform QC and alignment in parallel. Quality metrics were calculated using Picard CollectQualityYieldMetrics. uBAMs were converted to FASTQ using Picard SamToFastq and aligned to the Hg38 reference genome using BWA mem 0.7.15 with batch size set using -K 100000000. Metadata from the uBAMs was then merged with the aligned BAMs using Picard MergeBamAlignment with the parameters --SORT_ORDER="unsorted", allowing the data to be grouped by read name for efficient downstream marking of duplicates, and --UNMAP_CONTAMINANT_READS=true, to remove cross-species contamination.
+Whole genome paired-end reads in unmapped BAM (uBAM) format were first scattered to perform QC and alignment in parallel. Quality metrics were calculated using Picard CollectQualityYieldMetrics. uBAMs were converted to FASTQ using Picard SamToFastq and aligned to the Hg38 reference genome using BWA mem v0.7.15 with batch size set using -K 100000000. Metadata from the uBAMs was then merged with the aligned BAMs using Picard MergeBamAlignment with the parameters --SORT_ORDER="unsorted", allowing the data to be grouped by read name for efficient downstream marking of duplicates, and --UNMAP_CONTAMINANT_READS=true, to remove cross-species contamination.
 
 QC metrics (base distribution by cycle, insert size metrics, mean quality by cycle, and quality score distribution) were collected for the aligned, unsorted read-groups using Picard CollectMultipleMetrics. The read-group specific aligned BAMs were then aggregated and duplicate reads were flagged using Picard MarkDuplicates assuming queryname-sorted order and the parameter --OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500, which is appropriate for patterned flowcells.
 
@@ -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 3.0.0 pipeline using Picard 2.23.8, GATK 4.2.2.0, and Samtools 1.11 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 version 3.4.12. 
+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. 
 
 ### Pre-processing and quality control metrics
 
@@ -57,5 +57,6 @@ 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_v3.0.0](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)