Merge branch 'dorado-052' into 'dev'

Update Dorado to v0.5.2

See merge request epi2melabs/workflows/wf-basecalling!54

.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
+

.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

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

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 |
 |-------|-----------|-------------|--------------------------|

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:

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.
+

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 |
 |-------|-----------|-------------|--------------------------|

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 '[email protected]'",
             "--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 {