Merge pull request #106 from broadinstitute/staging

releasing SS2 with loom bug fix (#105)

dockers/skylab/loom-output/create_loom_ss2.py

@@ -51,9 +51,9 @@ def generate_col_attr(args):
     col_attrs["cell_names"] = [cell_id]
 
     if args.input_id_metadata_field:
-        col_attrs["input_id_metadata_field"] = args.input_id_metadata_field
+        col_attrs["input_id_metadata_field"] = [args.input_id_metadata_field]
     if args.input_name_metadata_field:
-            col_attrs["input_name_metadata_field"] = args.input_name_metadata_field
+            col_attrs["input_name_metadata_field"] = [args.input_name_metadata_field]
 
     numeric_field_names = np.array(sorted_numeric_labels[:])
     for i in range(0, numeric_field_names.shape[0]):

pipelines/broad/dna_seq/germline/single_sample/wgs/README.md

@@ -1,6 +1,6 @@
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [WholeGenomeGermlineSingleSample_v2.0](https://github.com/broadinstitute/warp/releases) | June 22, 2020 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [Kylee Degatano](mailto:[email protected]) |
+| [WholeGenomeGermlineSingleSample_v2.0](https://github.com/broadinstitute/warp/releases) | October 02, 2020 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [Kylee Degatano](mailto:[email protected]) |
 
 # Introduction to the Whole Genome Germline Single Sample Pipeline
 
@@ -18,7 +18,7 @@ The [Whole Genome Germline Single Sample workflow](WholeGenomeGermlineSingleSamp
 * Samtools 1.3.1
 * Python 2.7 and 3.0
 * Cromwell version support 
-    * Successfully tested on v47
+    * Tested on Cromwell 52
     * Does not work on versions < v23 due to output syntax
 
 
@@ -48,6 +48,7 @@ You can read more about the software tools implemented in these tasks by reading
 
 # Important Notes
 * The accompanying JSON is a generic, ready to use, example template for the workflow. It is the user’s responsibility to correctly set the reference and resource variables for their own particular test case using the [GATK Tool and Tutorial Documentations](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591).
+* By default, HaplotypeCaller will perform variant calling using GATK 3.5, which is what is used in Broad Production. To use GATK4, specify `use_gatk3_haplotype_caller=false` in the inputs.json.
 * Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
 * For help running workflows on the Google Cloud Platform or locally please
 view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).

pipelines/skylab/optimus/Optimus.changelog.md

@@ -1,3 +1,9 @@
+# 4.1.2
+
+2020-10-13 (Date of Last Commit)
+
+* Added a new docker in LoomUtils.wdl
+
 # 4.1.1
 
 2020-10-07 (Date of Last Commit)

pipelines/skylab/optimus/Optimus.wdl

@@ -56,7 +56,7 @@ workflow Optimus {
 
   # version of this pipeline
 
-  String pipeline_version = "4.1.1"
+  String pipeline_version = "4.1.2"
 
   # this is used to scatter matched [r1_fastq, r2_fastq, i1_fastq] arrays
   Array[Int] indices = range(length(r1_fastq))

pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md

@@ -1,3 +1,10 @@
+# 2.1.2
+
+2020-10-13 (Date of Last Commit)
+
+* Fixed a bug in the loom file generation script that appeared when using optional input `input_id_metadata_field`
+* Updated the docker in LoomUtils.wdl task to v0.0.3
+
 # 2.1.1
 
 2020-10-01 (Date of Last Commit)

pipelines/skylab/smartseq2_multisample/MultiSampleSmartSeq2.wdl

@@ -34,7 +34,7 @@ workflow MultiSampleSmartSeq2 {
       Boolean paired_end
   }
   # Version of this pipeline
-  String pipeline_version = "2.1.1"
+  String pipeline_version = "2.1.2"
 
   if (false) {
      String? none = "None"

pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md

@@ -1,3 +1,10 @@
+# 5.0.2
+
+2020-10-13 (Date of Last Commit)
+
+* Fixed a bug in the loom file generation script that appeared when using optional input `input_id_metadata_field`
+* Updated the docker in LoomUtils.wdl task to v0.0.3
+
 # 5.0.1
 
 2020-10-01 (Date of Last Commit)
@@ -90,4 +97,3 @@
 * No release note available
 
 
-

pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl

@@ -38,7 +38,7 @@ workflow SmartSeq2SingleCell {
   }
 
   # version of this pipeline
-  String pipeline_version = "5.0.1"
+  String pipeline_version = "5.0.2"
 
   parameter_meta {
     genome_ref_fasta: "Genome reference in fasta format"

tasks/skylab/LoomUtils.wdl

@@ -3,7 +3,7 @@ version 1.0
 task SmartSeq2LoomOutput {
   input {
     #runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3-fk-2"
+    String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3"
     # the gene count file "<input_id>_rsem.genes.results" in the task results folder call-RSEMExpression
     File rsem_gene_results
     # file named "<input_id>_QCs.csv" in the folder  "call-GroupQCOutputs/glob-*" of the the SS2  output
@@ -58,7 +58,7 @@ task OptimusLoomGeneration {
 
   input {
     #runtime values
-    String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3-fk-2"
+    String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3"
     # name of the sample
     String input_id
     # user provided id
@@ -143,7 +143,7 @@ task AggregateSmartSeq2Loom {
         String batch_id
         String? batch_name
         String pipeline_version
-        String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3-fk-2"
+        String docker = "quay.io/humancellatlas/secondary-analysis-loom-output:0.0.3"
         Int disk = 100
     }