Merge pull request #100 from broadinstitute/staging

Staging->Master
broadinstitute · Oct 7, 2020 · 3e08cd2 · 3e08cd2
2 parents 3b84df4 + 45ff267
commit 3e08cd2
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diff --git a/.dockstore.yml b/.dockstore.yml
@@ -15,3 +15,12 @@ workflows:
   - name: scATAC
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/scATAC/scATAC.wdl
+  - name: JointGenotyping
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
+  - name: ExomeGermlineSingleSample
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
+  - name: WholeGenomeGermlineSingleSample
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
diff --git a/dockers/skylab/optimus-test-matrix/Dockerfile b/dockers/skylab/optimus-test-matrix/Dockerfile
@@ -1,10 +1,12 @@
 # Start with an ubuntu system and update it
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 # Image label
 LABEL maintainer="Lantern Team <[email protected]>" \
   software="Optimus Matrix Tester" 
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 # Enable source repositories to install deps for R and update the apt-get list
 RUN sed -Ei 's/^# deb-src /deb-src /' /etc/apt/sources.list && apt-get update
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.2.0
+2020-10-01
+
+* Updated task definitions to include a new tool not currently used in Arrays wdl
+
 # 2.1.0
 2020-08-18
 

diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow Arrays {
 
-  String pipeline_version = "2.1.0"
+  String pipeline_version = "2.2.0"
 
   input {
 

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md
@@ -1,3 +1,8 @@
+# 1.11.0
+2020-10-01
+
+* Updated task definitions to include a new tool not currently used in ValidateChip wdl
+
 # 1.10.0
 2020-08-18
 

diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl
@@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks
 
 workflow ValidateChip {
 
-  String pipeline_version = "1.10.0"
+  String pipeline_version = "1.11.0"
 
   input {
     String sample_alias

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,3 +1,8 @@
+# 1.11.0
+2020-10-01
+
+* Added use of BafRegress to the pipeline.  BafRegress detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.
+
 # 1.10.0
 2020-08-18
 

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.documentation.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.documentation.md
@@ -1,6 +1,6 @@
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [Version 1.9](IlluminaGenotypingArray.wdl) | July 31, 2020 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in warp or contact [Kylee Degatano](mailto:[email protected]) |
+| [Version 1.11.0](IlluminaGenotypingArray.wdl) | Oct 1, 2020 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in warp or contact [Kylee Degatano](mailto:[email protected]) |
 
 # Table of Contents
 - [Illumina Genotyping Array Pipeline Overview](#illumina-genotyping-array-pipeline-overview)
@@ -97,6 +97,7 @@ The workflow requires that each input is specified in a JSON file. All sample an
 | Input name | Description | Required or Optional | Input format |
 | --- | --- | --- | --- |
 | call_rate_threshold | Minimal numeric value for a sample to have a passing call rate | Required | Value | 
+| minor_allele_frequency_file | Cloud path to a chip-specific text file containing locus-id to minor allele frequency | Optional | String |
 | contamination_controls_vcf | Cloud path to a VCF of samples run on this chip type to be used to supplement contamination calling | Optional | String |
 | subsampled_metrics_interval_list | Cloud path to a file containing a subset sites for which the workflow generate metrics and outputs a VCF | Optional | String | 
 | disk_size | Default disk (in GiB) for this workflow's cloud VMs | Required | Value | 
@@ -115,6 +116,7 @@ The following table provides a summary of the tasks and tools called by the Illu
 | --- | --- | --- |
 | Autocall | [iaap-cli gencall](https://support.illumina.com/downloads/iaap-genotyping-cli.html) | Illumina |
 | GtcToVcf | [GtcToVcf](https://gatk.broadinstitute.org/hc/en-us/articles/360037595031-GtcToVcf-Picard-) | Picard |
+| BafRegress | [BafRegress](https://genome.sph.umich.edu/wiki/BAFRegress) | https://genome.sph.umich.edu/wiki/File:BafRegress.tar.gz |
 | VcfToAdpc | [VcfToAdpc](https://gatk.broadinstitute.org/hc/en-us/articles/360036484712-VcfToAdpc-Picard-) | Picard |
 | VerifyIDIntensity | [VerifyIDIntensity](https://github.com/gjun/verifyIDintensity) | https://github.com/gjun/verifyIDintensity |
 | CreateVerifyIDIntensityContaminationMetricsFile | [CreateVerifyIDIntensityContaminationMetricsFile](https://gatk.broadinstitute.org/hc/en-us/articles/360036805271) | Picard |
@@ -150,7 +152,13 @@ Illumina BeadChip Genotyping technology demarcates small-nucleotide variants (an
 After genoytping, the workflow calls the GtcToVcf task, which runs the Picard tool [GtcToVcf](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_GtcToVcf.php) to convert the GTC into a VCF. 
 
 ### 2. Contamination Detection
-Intra-species DNA contamination is a common problem for genotyping samples. To detect contamination, the Illumina Array workflow uses the software [VerifyIDIntensity](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487130/), which requires an 'adpc.bin' file (a binary file containing array intensity data that can be used with Illumina software) as input. The workflow first calls the [VcfToAdpc](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_VcfToAdpc.php) task to convert the VCF output from  genotype calling into an 'adpc.bin' file.  Next, the [VerifyIDIntensity](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487130/) task uses this input file to measure contamination. The [CreateVerifyIDIntensityContaminationMetricsFile](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_CreateVerifyIDIntensityContaminationMetricsFile.php) task then converts the VerifyIDIntensity output into a Picard-standard metrics file (chip_well_barcode.verifyidintensity_metrics), suitable for uploading to a metrics database.
+Intra-species DNA contamination is a common problem for genotyping samples.
+
+The Illumina Array workflow uses two tools to detect contamination.  These are BafRegress and VerifyIDIntensity.  The use of VerifyIDIntensity is deprecated as it can overestimate estimated contamination when used in single-sample mode (as it is run typically)
+
+[BafRegress](https://genome.sph.umich.edu/wiki/BAFRegress) is a software that detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.  It requires a file formatted as an Illumina Final Report.  The workflow takes care of this in the BafRegress task (which contains functionality to both create the Illumina Final Report from the VCF generated by GtcToVcf and then run the BafRegress tool itself.  The output of a BafRegress task is a text file containing the estimated contamination along with associated metrics.
+
+[VerifyIDIntensity](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487130/) requires an 'adpc.bin' file (a binary file containing array intensity data that can be used with Illumina software) as input. The workflow first calls the [VcfToAdpc](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_VcfToAdpc.php) task to convert the VCF output from  genotype calling into an 'adpc.bin' file.  Next, the [VerifyIDIntensity](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487130/) task uses this input file to measure contamination. The [CreateVerifyIDIntensityContaminationMetricsFile](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_CreateVerifyIDIntensityContaminationMetricsFile.php) task then converts the VerifyIDIntensity output into a Picard-standard metrics file (chip_well_barcode.verifyidintensity_metrics), suitable for uploading to a metrics database.
 
 ### 3. Rare Variant Calling (Optional)
 After running default genotype processing with Autocall, the Illumina Genotyping Array workflow optionally uses the [zCall](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463112/) task to improve calls on rare variants. To run this task, the workflow requires a zCall threshold file. If the workflow identifies the file, it will output a PLINK .ped and .map file. The [MergePedIntoVcf](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_arrays_MergePedIntoVcf.php) task then merges these outputs into the VCF generated during genotype calling. 
@@ -182,6 +190,7 @@ The tables below summarize all of the workflow's output according to task. Outpu
 | chip_well_barcode.vcf.gz | VCF generated by the pipeline | Required | Compressed VCF (vcf.gz) |
 | chip_well_barcode.vcf.gz.tbi | Index file of the VCF generated by the pipeline | Required | tabix index (vcf.gz.tbi) |
 | chip_well_barcode.gtc | GTC file generated by Autocall | Required | GTC |
+| chip_well_barcode.bafregress_metrics | Text output file generated by BafRegress | Optional | txt |
 | chip_well_barcode.verifyidintensity_metrics | File containing metrics generated by VerifyIDIntensity | Required | txt |
 | chip_well_barcode.arrays_variant_calling_detail_metrics | Detailed metrics file for the output VCF generated by CollectArraysVariantCallingMetrics.detail_metrics | Required | txt | 
 | chip_well_barcode.arrays_variant_calling_summary_metrics | Summary metrics file for the output VCF as generated by CollectArraysVariantCallingMetrics | Required | txt |

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
@@ -20,7 +20,7 @@ import "../../../../tasks/broad/IlluminaGenotypingArrayTasks.wdl" as GenotypingT
 
 workflow IlluminaGenotypingArray {
 
-  String pipeline_version = "1.10.0"
+  String pipeline_version = "1.11.0"
 
   input {
 
@@ -64,6 +64,9 @@ workflow IlluminaGenotypingArray {
     # For Contamination Checking
     File? contamination_controls_vcf
 
+    # For BAFRegress
+    File? minor_allele_frequency_file
+
     # For HapMap GenotypeConcordance Check:
     File? control_sample_vcf_file
     File? control_sample_vcf_index_file
@@ -134,6 +137,18 @@ workflow IlluminaGenotypingArray {
         pipeline_version = "IlluminaGenotypingArray_v" + pipeline_version
     }
 
+    if (defined(minor_allele_frequency_file)) {
+      call GenotypingTasks.BafRegress {
+        input:
+          input_vcf = GtcToVcf.output_vcf,
+          input_vcf_index = GtcToVcf.output_vcf_index,
+          maf_file = minor_allele_frequency_file,
+          output_results_filename = chip_well_barcode + ".results.txt",
+          disk_size = disk_size,
+          preemptible_tries = preemptible_tries,
+      }
+    }
+
     call GenotypingTasks.VcfToAdpc {
       input:
         input_vcf = GtcToVcf.output_vcf,
@@ -326,6 +341,7 @@ workflow IlluminaGenotypingArray {
     File? output_vcf_md5_cloud_path = VcfMd5Sum.md5_cloud_path
     File? output_vcf = final_output_vcf
     File? output_vcf_index = final_output_vcf_index
+    File? bafregress_results_file = BafRegress.results_file
     File? contamination_metrics = CreateVerifyIDIntensityContaminationMetricsFile.output_metrics_file
     File? output_fingerprint_vcf = SelectFingerprintVariants.output_vcf
     File? output_fingerprint_vcf_index = SelectFingerprintVariants.output_vcf_index

diff --git a/pipelines/broad/genotyping/illumina/test_inputs/Scientific/204126290052_R01C01_NA12878.json b/pipelines/broad/genotyping/illumina/test_inputs/Scientific/204126290052_R01C01_NA12878.json
@@ -26,5 +26,6 @@
   "IlluminaGenotypingArray.dbSNP_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi",
   "IlluminaGenotypingArray.haplotype_database_file": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt",
   "IlluminaGenotypingArray.variant_rsids_file": "gs://broad-references-private/hg19/v0/Homo_sapiens_assembly19.haplotype_database.snps.list",
+  "IlluminaGenotypingArray.minor_allele_frequency_file": "gs://broad-gotc-test-storage/arrays/metadata/GDA-8v1-0_A5/GDA-8v1-0_A5.MAF.txt",
   "IlluminaGenotypingArray.preemptible_tries": 3
 }
diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 2.1.1
+2020-10-01
+
+* Removed extra trailing slash in ouput directory from cloud to cloud copy job
+
 # 2.1.0
 2020-08-18
 

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl
@@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
 
 workflow ExternalExomeReprocessing {
 
-  String pipeline_version = "2.1.0"
+  String pipeline_version = "2.1.1"
 
   input {
     File? input_cram

diff --git a/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.1
+2020-10-01
+
+* Removed extra trailing slash in ouput directory from cloud to cloud copy job
+
 # 1.1.0
 2020-08-18
 

diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl
@@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy
 
 workflow ExternalWholeGenomeReprocessing {
 
-  String pipeline_version = "1.1.0"
+  String pipeline_version = "1.1.1"
 
   input {
     File? input_cram

diff --git a/pipelines/skylab/optimus/Optimus.changelog.md b/pipelines/skylab/optimus/Optimus.changelog.md
@@ -1,9 +1,17 @@
+# 4.1.0
+
+2020-10-05 (Date of Last Commit)
+
+* Updated sctools dockers and made them consistent across the Optimus pipeline
+
+
 # 4.0.2
 
 2020-09-30 (Date of Last Commit)
 
 * Corrected the path to the FastqProcessing WDL
 
+
 # 4.0.1
 
 2020-09-28 (Date of Last Commit)

diff --git a/pipelines/skylab/optimus/Optimus.wdl b/pipelines/skylab/optimus/Optimus.wdl
@@ -58,7 +58,7 @@ workflow Optimus {
   }
 
   # version of this pipeline
-  String pipeline_version = "4.0.2"
+  String pipeline_version = "4.1.0"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))

diff --git a/tasks/broad/CopyFilesFromCloudToCloud.wdl b/tasks/broad/CopyFilesFromCloudToCloud.wdl
@@ -50,7 +50,7 @@ task CopyFilesFromCloudToCloud {
         ((count++)) && ((count >= $RETRY_LIMIT)) && break
     done
     if ! grep -q no_contamination contamination; then
-      /usr/local/google-cloud-sdk/bin/gsutil -m cp -L cp.log contamination ~{destination_cloud_path}/~{base_file_name}.contamination
+      /usr/local/google-cloud-sdk/bin/gsutil -m cp -L cp.log contamination ~{destination_cloud_path}~{base_file_name}.contamination
     fi
     if [ "$count" -ge "$RETRY_LIMIT" ]; then
         echo 'Could not copy all the files to the cloud destination' && exit 1

diff --git a/tasks/broad/IlluminaGenotypingArrayTasks.wdl b/tasks/broad/IlluminaGenotypingArrayTasks.wdl
@@ -143,6 +143,36 @@ task GtcToVcf {
   }
 }
 
+task BafRegress {
+  input {
+    File input_vcf
+    File input_vcf_index
+    File? maf_file
+    String output_results_filename
+
+    Int disk_size
+    Int preemptible_tries
+  }
+
+  command {
+    set -eo pipefail
+
+    /root/tools/bcftools/bin/bcftools view -f 'PASS,.' ~{input_vcf} 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 | python /root/tools/parseVcfToBAFRegress.py > temp.final_report.txt
+
+    python /root/tools/bafRegress.py estimate --freqfile ~{maf_file} temp.final_report.txt > ~{output_results_filename}
+  }
+  runtime {
+    docker: "us.gcr.io/broad-gotc-prod/bafregress:1.0"
+    disks: "local-disk " + disk_size + " HDD"
+    memory: "3.5 GiB"
+    preemptible: preemptible_tries
+  }
+
+  output {
+    File results_file = output_results_filename
+  }
+}
+
 task VcfToAdpc {
   input {
     File input_vcf

diff --git a/tasks/skylab/Attach10xBarcodes.wdl b/tasks/skylab/Attach10xBarcodes.wdl
@@ -9,7 +9,7 @@ task Attach10xBarcodes {
     String chemistry
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.4"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 48000
     Int cpu = 2
     # estimate that bam is approximately the size of all inputs plus 50%

diff --git a/tasks/skylab/CreateCountMatrix.wdl b/tasks/skylab/CreateCountMatrix.wdl
@@ -6,7 +6,7 @@ task CreateSparseCountMatrix {
     File gtf_file
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.7"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 8250
     Int cpu = 1
     Int disk = ceil(size(bam_input, "Gi") + size(gtf_file, "Gi")) * 4 + 10
@@ -62,7 +62,7 @@ task MergeCountFiles {
     Array[File] col_indices
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.7"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 8250
     Int cpu = 1
     Int disk = 20  # todo find out how to make this adaptive with Array[file] input

diff --git a/tasks/skylab/FastqProcessing.wdl b/tasks/skylab/FastqProcessing.wdl
@@ -10,7 +10,7 @@ task FastqProcessing {
     String sample_id
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.10"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 3850
     Int cpu = 16   
     #TODO decided cpu

diff --git a/tasks/skylab/SequenceDataWithMoleculeTagMetrics.wdl b/tasks/skylab/SequenceDataWithMoleculeTagMetrics.wdl
@@ -5,8 +5,8 @@ task CalculateGeneMetrics {
     File bam_input
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.7"
-    Int machine_mem_mb = 8000
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
+    Int machine_mem_mb = 22000
     Int cpu = 1
     Int disk = ceil(size(bam_input, "Gi") * 4)
     Int preemptible = 3
@@ -50,8 +50,8 @@ task CalculateCellMetrics {
     File original_gtf
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.8"
-    Int machine_mem_mb = 8000
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
+    Int machine_mem_mb = 45000
     Int cpu = 1
     Int disk = ceil(size(bam_input, "Gi") * 2)
     Int preemptible = 3
@@ -95,8 +95,8 @@ task MergeGeneMetrics {
     Array[File] metric_files
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.7"
-    Int machine_mem_mb = 8000
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
+    Int machine_mem_mb = 3850
     Int cpu = 1
     Int disk = 20
     Int preemptible = 3
@@ -139,8 +139,8 @@ task MergeCellMetrics {
     Array[File] metric_files
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.7"
-    Int machine_mem_mb = 8000
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
+    Int machine_mem_mb = 3850
     Int cpu = 1
     Int disk = 20
     Int preemptible = 3

diff --git a/tasks/skylab/SplitBamByCellBarcode.wdl b/tasks/skylab/SplitBamByCellBarcode.wdl
@@ -6,7 +6,7 @@ task SplitBamByCellBarcode {
     Float size_in_mb = 1024.0
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.5"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
 
     Int machine_mem_mb = 15258
     Int cpu = 16

diff --git a/tasks/skylab/TagSortBam.wdl b/tasks/skylab/TagSortBam.wdl
@@ -5,7 +5,7 @@ task CellSortBam {
     File bam_input
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.2"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 100000
     Int cpu = 2
     Int disk = ceil(size(bam_input, "Gi") * 8)
@@ -49,7 +49,7 @@ task GeneSortBam {
     File bam_input
 
     # runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.2"
+    String docker = "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11"
     Int machine_mem_mb = 100000
     Int cpu = 2
     Int disk = ceil(size(bam_input, "Gi") * 4)

diff --git a/tests/skylab/optimus/pr/ValidateOptimus.wdl b/tests/skylab/optimus/pr/ValidateOptimus.wdl
@@ -173,7 +173,7 @@ task ValidateMatrix {
     >>>
 
     runtime {
-        docker: "quay.io/humancellatlas/optimus-matrix-test:0.0.4"
+        docker: "quay.io/humancellatlas/optimus-matrix-test:0.0.7"
         cpu: 1
         memory: "16 GB"
         disks: "local-disk ${required_disk} HDD"
-Original file line number
+Diff line change
@@ -1,3 +1,8 @@
+    # 2.2.0
+-10-01
+    * Updated task definitions to include a new tool not currently used in Arrays wdl
     # 2.1.0
 -08-18
@@ Expand Down @@