From 553e312b0ff06245de121107f8971875e37742ee Mon Sep 17 00:00:00 2001 From: Sam Nicholls Date: Mon, 22 Jan 2024 18:16:07 +0000 Subject: [PATCH] Update Dorado to v0.5.2 --- .github/ISSUE_TEMPLATE/bug_report.yml | 19 +++++++++++++++++++ .pre-commit-config.yaml | 4 ++-- CHANGELOG.md | 4 ++++ README.md | 13 +++++++++++-- bin/workflow_glue/check_sample_sheet.py | 2 +- docs/06_input_example.md | 3 +++ docs/{06_inputs.md => 06_input_parameters.md} | 0 docs/07_outputs.md | 2 +- nextflow.config | 6 +++--- 9 files changed, 44 insertions(+), 9 deletions(-) create mode 100644 docs/06_input_example.md rename docs/{06_inputs.md => 06_input_parameters.md} (100%) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index d8f9579..f2c8a55 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -122,3 +122,22 @@ body: render: shell validations: required: false + - type: dropdown + id: run-demo + attributes: + label: Were you able to successfully run the latest version of the workflow with the demo data? + description: For CLI execution, were you able to successfully run the workflow using the demo data available in the [Install and run](./README.md#install-and-run) section of the `README.md`? For execution in the EPI2ME application, were you able to successfully run the workflow via the "Use demo data" button? + options: + - yes + - no + - other (please describe below) + validations: + required: true + - type: textarea + id: demo-other + attributes: + label: Other demo data information + render: shell + validations: + required: false + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8134142..2ca2e89 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,12 +3,12 @@ repos: hooks: - id: docs_readme name: docs_readme - entry: parse_docs -p docs -e .md -s 01_brief_description 02_introduction 03_compute_requirements 04_install_and_run 05_related_protocols 06_inputs 07_outputs 08_pipeline_overview 09_troubleshooting 10_FAQ 11_other -ot README.md -od output_definition.json -ns nextflow_schema.json + entry: parse_docs -p docs -e .md -s 01_brief_description 02_introduction 03_compute_requirements 04_install_and_run 05_related_protocols 06_input_example 06_input_parameters 07_outputs 08_pipeline_overview 09_troubleshooting 10_FAQ 11_other -ot README.md -od output_definition.json -ns nextflow_schema.json language: python always_run: true pass_filenames: false additional_dependencies: - - epi2melabs>=0.0.50 + - epi2melabs>=0.0.51 - id: build_models name: build_models entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 8046402..cc5efc4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [v1.1.4] +### Changed +- Updated Dorado to v0.5.2 (see https://github.com/nanoporetech/dorado/releases/tag/v0.5.2) + ## [v1.1.3] ### Changed - Bumped memory directives for intense tasks to reduce likelihood of job failure diff --git a/README.md b/README.md index 87a0e87..430c20c 100644 --- a/README.md +++ b/README.md @@ -89,7 +89,16 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec -## Inputs +## Input example + +This workflow accepts a folder containing FAST5 or POD5 files as input. +The folder may contain other folders of FAST5 or POD5 files and all files will be processed by the workflow. + + + + + +## Input parameters ### Input Options @@ -164,7 +173,7 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec ## Outputs -Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. +Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. | Title | File path | Description | Per sample or aggregated | |-------|-----------|-------------|--------------------------| diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py index fe4fc37..62e3483 100755 --- a/bin/workflow_glue/check_sample_sheet.py +++ b/bin/workflow_glue/check_sample_sheet.py @@ -43,7 +43,7 @@ def main(args): ] if not os.path.exists(args.sample_sheet) or not os.path.isfile(args.sample_sheet): - sys.stdout.write(f"Could not open sample sheet '{args.sample_sheet}'.") + sys.stdout.write("Could not open sample sheet file.") sys.exit() try: diff --git a/docs/06_input_example.md b/docs/06_input_example.md new file mode 100644 index 0000000..c60c4e8 --- /dev/null +++ b/docs/06_input_example.md @@ -0,0 +1,3 @@ +This workflow accepts a folder containing FAST5 or POD5 files as input. +The folder may contain other folders of FAST5 or POD5 files and all files will be processed by the workflow. + diff --git a/docs/06_inputs.md b/docs/06_input_parameters.md similarity index 100% rename from docs/06_inputs.md rename to docs/06_input_parameters.md diff --git a/docs/07_outputs.md b/docs/07_outputs.md index f5a8ea5..af38d0d 100644 --- a/docs/07_outputs.md +++ b/docs/07_outputs.md @@ -1,4 +1,4 @@ -Outputs files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. +Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}. | Title | File path | Description | Per sample or aggregated | |-------|-----------|-------------|--------------------------| diff --git a/nextflow.config b/nextflow.config index caa86dd..96f8cc4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -57,8 +57,8 @@ params { wf { basecaller_container = "ontresearch/dorado" - container_sha = "shab1ff19616e2b8635791f17bef11f806628505a35" - common_sha = "sha399b89c275a4d8eac477a415691cb93180661be6" + container_sha = "shac28cd94f2303b0493a4b16ca86e711852c2b8525" + common_sha = "sha1c5febff9f75143710826498b093d9769a5edbb9" example_cmd = [ "--basecaller_cfg 'dna_r10.4.1_e8.2_400bps_hac@v4.1.0'", "--dorado_ext 'pod5'", @@ -77,7 +77,7 @@ manifest { description = 'Helper workflow for basecalling ONT reads.' mainScript = 'main.nf' nextflowVersion = '>=23.04.2' - version = '1.1.3' + version = '1.1.4' } epi2melabs {