v2.3.0 final changes

README.md

@@ -55,7 +55,6 @@ You can expect a careful review of every PR and feedback as needed before mergin
 * **Michal Babinski** ([@Michal-Babins](https://github.com/Michal-Babins)) - Software, Validation
 * **Andrew Lang** ([@AndrewLangVt](https://github.com/AndrewLangVt)) - Software, Supervision
 * **Kelsey Kropp** ([@kelseykropp](https://github.com/kelseykropp)) - Validation
-* **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1)) - Validation
 * **Joel Sevinsky** ([@sevinsky](https://github.com/sevinsky)) - Conceptualization, Project Administration, Supervision
 
 ### External Contributors
@@ -68,6 +67,7 @@ We would like to gratefully acknowledge the following individuals from the publi
 * **Ash O'Farrel** ([@aofarrel](https://github.com/aofarrel))
 * **Sam Baird** ([@sam-baird](https://github.com/sam-baird))
 * **Holly Halstead** ([@HNHalstead](https://github.com/HNHalstead))
+* **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1))
 
 ### Maintaining PHB Pipelines
 

docs/index.md

@@ -46,7 +46,7 @@ When undertaking genomic analysis using the command-line, via Terra, or other da
 We continuously work to improve our codebase and usability of our workflows by the public health community, so changes from version to version are expected.  This documentation page reflects the state of the workflow at the version stated in the title.
 
 !!! dna "What's new?"
-    You can see the changes since PHB v2.2.0 [**here**](https://theiagen.notion.site/Public-Health-Bioinformatics-v2-2-1-Patch-Release-Notes-104cb013bc9380bcbd70dab04bf671a8?pvs=74)!
+    You can see the changes since PHB v2.2.1 [**here**](https://theiagen.notion.site/public-health-bioinformatics-v2-3-0-minor-release-notes?pvs=4)!
 
 ## Contributing to the PHB Repository
 
@@ -73,7 +73,6 @@ You can expect a careful review of every PR and feedback as needed before mergin
 - **Michal Babinski** ([@Michal-Babins](https://github.com/Michal-Babins)) - Software, Validation
 - **Andrew Lang** ([@AndrewLangVt](https://github.com/AndrewLangVt)) - Software, Supervision
 - **Kelsey Kropp** ([@kelseykropp](https://github.com/kelseykropp)) - Validation
-- **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1)) - Validation
 - **Joel Sevinsky** ([@sevinsky](https://github.com/sevinsky)) - Conceptualization, Project Administration, Supervision
 
 ### External Contributors
@@ -86,6 +85,7 @@ We would like to gratefully acknowledge the following individuals from the publi
 - **Ash O'Farrel** ([@aofarrel](https://github.com/aofarrel))
 - **Sam Baird** ([@sam-baird](https://github.com/sam-baird))
 - **Holly Halstead** ([@HNHalstead](https://github.com/HNHalstead))
+- **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1))
 
 ### On the Shoulder of Giants
 

docs/workflows/genomic_characterization/theiaeuk.md

@@ -69,7 +69,7 @@ All input reads are processed through "core tasks" in each workflow. The core ta
 | merlin_magic | **staphopia_sccmec_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0 | Do Not Modify, Optional |
 | merlin_magic | **tbp_parser_coverage_threshold** | Int | Internal component, do not modify | 100 | Do Not Modify, Optional |
 | merlin_magic | **tbp_parser_debug** | Boolean | Internal component, do not modify | FALSE | Do Not Modify, Optional |
-| merlin_magic | **tbp_parser_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.3.6 | Do Not Modify, Optional |
+| merlin_magic | **tbp_parser_docker_image** | String | Internal component, do not modify | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2 | Do Not Modify, Optional |
 | merlin_magic | **tbp_parser_min_depth** | Int | Internal component, do not modify | 10 | Do Not Modify, Optional |
 | merlin_magic | **tbp_parser_operator** | String | Internal component, do not modify | "Operator not provided" | Do Not Modify, Optional |
 | merlin_magic | **tbp_parser_output_seq_method_type** | String | Internal component, do not modify | "WGS" | Do Not Modify, Optional |

docs/workflows/genomic_characterization/theiaprok.md

@@ -418,7 +418,7 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al
 | merlin_magic | **tbp_parser_coverage_regions_bed** | File | A bed file that lists the regions to be considered for QC |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_coverage_threshold** | Int | The minimum coverage for a region to pass QC in tbp_parser | 100 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_debug** | Boolean | Activate the debug mode on tbp_parser; increases logging outputs | TRUE | Optional | FASTA, ONT, PE, SE |
-| merlin_magic | **tbp_parser_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.1.1 | Optional | FASTA, ONT, PE, SE |
+| merlin_magic | **tbp_parser_docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_etha237_frequency** | Float | Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser | 0.1 | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_expert_rule_regions_bed** | File | A file that contains the regions where R mutations and expert rules are applied |  | Optional | FASTA, ONT, PE, SE |
 | merlin_magic | **tbp_parser_min_depth** | Int | Minimum depth for a variant to pass QC in tbp_parser | 10 | Optional | FASTA, ONT, PE, SE |

docs/workflows/standalone/tbprofiler_tngs.md

@@ -23,7 +23,7 @@ This workflow is still in experimental research stages. Documentation is minimal
 | tbp_parser | **coverage_threshold** | Int | The minimum percentage of a region to exceed the minimum depth for a region to pass QC in tbp_parser | 100 | Optional |
 | tbp_parser | **cpu** | Int | Number of CPUs to allocate to the task | 1 | Optional |
 | tbp_parser | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
-| tbp_parser | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.1.1 | Optional |
+| tbp_parser | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2 | Optional |
 | tbp_parser | **etha237_frequency** | Float | Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser | 0.1 | Optional |
 | tbp_parser | **expert_rule_regions_bed** | File | A file that contains the regions where R mutations and expert rules are applied |  | Optional |
 | tbp_parser | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |

tasks/species_typing/mycobacterium/task_tbp_parser.wdl

@@ -31,7 +31,7 @@ task tbp_parser {
 
     Int cpu = 1
     Int disk_size = 100   
-    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.1"
+    String docker = "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.2.2"
     Int memory = 4
   }
   command <<<

tasks/task_versioning.wdl

@@ -9,7 +9,7 @@ task version_capture {
     volatile: true
   }
   command {
-    PHB_Version="PHB v2.2.1"
+    PHB_Version="PHB v2.3.0"
     ~{default='' 'export TZ=' + timezone}
     date +"%Y-%m-%d" > TODAY
     echo "$PHB_Version" > PHB_VERSION

tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml

@@ -22,7 +22,7 @@
     - path: miniwdl_run/call-raw_check_reads/task.log
     # trimmomatic
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/command
-      md5sum: fcc0e853c3719e41f3d169c291dc3927
+      md5sum: e16dcea259c3bf45ec374c92da0bf2dd
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/inputs.json
       contains: ["read1", "read2", "samplename"]
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/outputs.json

tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml

@@ -544,7 +544,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/multi/task_ts_mlst.wdl
       md5sum: ff8070a06eca94264ad6a7d91cb03bf0
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: 72d7f4462417909d85f692615e3a658b
+      md5sum: 92516e789845ffe5d883e03b3e767857
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 2aa70eab24868920f6c28843dd3b5613
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_kraken2.wdl

tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml

@@ -512,7 +512,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/multi/task_ts_mlst.wdl
       md5sum: ff8070a06eca94264ad6a7d91cb03bf0
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: 72d7f4462417909d85f692615e3a658b
+      md5sum: 92516e789845ffe5d883e03b3e767857
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 2aa70eab24868920f6c28843dd3b5613
     - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_kraken2.wdl