From 4fbb73e242c692a902aaeb5ae2f8c6362a9db7c4 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Mon, 16 Dec 2024 14:40:36 -0500 Subject: [PATCH] v2.3.0 final changes (#693) * update version tags * update md5sums * update default tbp-parser docker in docs --- README.md | 2 +- docs/index.md | 4 ++-- docs/workflows/genomic_characterization/theiaeuk.md | 2 +- docs/workflows/genomic_characterization/theiaprok.md | 2 +- docs/workflows/standalone/tbprofiler_tngs.md | 2 +- tasks/species_typing/mycobacterium/task_tbp_parser.wdl | 2 +- tasks/task_versioning.wdl | 2 +- tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 10 files changed, 11 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 138a1868c..d4f1dea8e 100644 --- a/README.md +++ b/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 diff --git a/docs/index.md b/docs/index.md index ad825cfa3..49a4ee157 100644 --- a/docs/index.md +++ b/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 diff --git a/docs/workflows/genomic_characterization/theiaeuk.md b/docs/workflows/genomic_characterization/theiaeuk.md index 2bfc2e6cf..bdfeb5d81 100644 --- a/docs/workflows/genomic_characterization/theiaeuk.md +++ b/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 | diff --git a/docs/workflows/genomic_characterization/theiaprok.md b/docs/workflows/genomic_characterization/theiaprok.md index d3dbb55b0..41e11c51b 100644 --- a/docs/workflows/genomic_characterization/theiaprok.md +++ b/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 | diff --git a/docs/workflows/standalone/tbprofiler_tngs.md b/docs/workflows/standalone/tbprofiler_tngs.md index 96f29e0bf..b9bec3abe 100644 --- a/docs/workflows/standalone/tbprofiler_tngs.md +++ b/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 | diff --git a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl b/tasks/species_typing/mycobacterium/task_tbp_parser.wdl index 60baa0b99..3ccdb6d0d 100644 --- a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl +++ b/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 <<< diff --git a/tasks/task_versioning.wdl b/tasks/task_versioning.wdl index fab908614..04b9c5b11 100644 --- a/tasks/task_versioning.wdl +++ b/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 diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml index d2e0c64f9..444c41b5d 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml +++ b/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 diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 58f0b6fb4..d9dfb5218 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/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 diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index 06caae04d..2b6580c82 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/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