Merge branch 'template_updates_2024-01-12' into 'dev'

Template updates 2024 01 12

See merge request epi2melabs/workflows/wf-transcriptomes!150

.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

README.md

@@ -83,7 +83,31 @@ Find related protocols in the [Nanopore community](https://community.nanoporetec
 
 
 
-## Inputs
+## Input example
+
+<!---Example of input directory structure, delete and edit as appropriate per workflow.--->
+This workflow accepts FASTQ files as input.
+
+The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates).
+
+```
+(i)                     (ii)                 (iii)    
+input_reads.fastq   ─── input_directory  ─── input_directory
+                        ├── reads0.fastq     ├── barcode01
+                        └── reads1.fastq     │   ├── reads0.fastq
+                                             │   └── reads1.fastq
+                                             ├── barcode02
+                                             │   ├── reads0.fastq
+                                             │   ├── reads1.fastq
+                                             │   └── reads2.fastq
+                                             └── barcode03
+                                              └── reads0.fastq
+```
+
+
+
+
+## Input parameters
 
 ### Input Options
 
@@ -163,7 +187,7 @@ 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 +1,18 @@
+<!---Example of input directory structure, delete and edit as appropriate per workflow.--->
+This workflow accepts FASTQ files as input.
+
+The FASTQ input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. If you are using the workflow for differential expression analysis the last case(iii) will be expected with a minimum of 4 samples (at least 2 replicates of each sample to compare) but we recommend 6 samples (three replicates).
+
+```
+(i)                     (ii)                 (iii)    
+input_reads.fastq   ─── input_directory  ─── input_directory
+                        ├── reads0.fastq     ├── barcode01
+                        └── reads1.fastq     │   ├── reads0.fastq
+                                             │   └── reads1.fastq
+                                             ├── barcode02
+                                             │   ├── reads0.fastq
+                                             │   ├── reads1.fastq
+                                             │   └── reads2.fastq
+                                             └── barcode03
+                                              └── reads0.fastq
+```

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

@@ -105,7 +105,7 @@ params {
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"
-    common_sha = "sha399b89c275a4d8eac477a415691cb93180661be6"
+	common_sha = "sha1c5febff9f75143710826498b093d9769a5edbb9"
     }
 }