Merge branch 'CW-790' into 'dev'

template updates

See merge request epi2melabs/workflow-containers/wf-artic!113

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,76 @@
+name: Bug Report
+description: File a bug report
+title: "[Bug]: "
+labels: ["bug", "triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: Tell us what you see!
+      value: "A bug happened!"
+    validations:
+      required: true
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating System
+      description: What operating system are you running?
+      options:
+        - Windows 10
+        - Windows 11
+        - macOS
+        - ubuntu 18.04
+        - ubuntu 20.04
+    validations:
+      required: true
+  - type: dropdown
+    id: execution
+    attributes:
+      label: Workflow Execution
+      description: Where are you running the workflow?
+      options:
+        - EPI2ME Labs desktop application
+        - Command line
+        - EPI2ME
+        - Other (please describe)
+    validations:
+      required: true
+  - type: input
+    id: labs-version
+    attributes:
+      label: Workflow Execution - EPI2ME Labs Versions
+      description: If you're running using EPI2ME Labs please provide the version and the environment version (Click the blue help icon bottom left and select ":bout")?
+    validations:
+      required: false
+  - type: dropdown
+    id: profile
+    attributes:
+      label: Workflow Execution - Execution Profile
+      description: If you're using the CLI to run the workflow, what profile are you using?
+      options:
+        - Docker
+        - Singularity
+        - Conda
+    validations:
+      required: false
+  - type: input
+    id: version
+    attributes:
+      label: Workflow Version
+      description: What version of the workflow are you running?
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: shell
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+    - name: Nanopore customer support
+      url: https://nanoporetech.com/contact
+      about: For general support, including bioinformatics questions.

.gitlab-ci.yml

@@ -4,6 +4,7 @@ include:
 
 variables:
     NF_WORKFLOW_OPTS: "--fastq test_data/fastq --samples test_data/sample_sheet.csv"
+    NF_IGNORE_PROCESSES: "checkSampleSheet,combineGenotypeSummaries,genotypeSummary,report_no_data"
     IMAGE_TAG: "NO_UPDATE"
 
 check-versions:

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.17]
+### Changes
+- Args parser for fastqingress
+- Set out_dir option type to ensure output is written to correct directory on Windows
+
 ## [v0.3.16]
 ### Added
 - `--pangolin_options` command line arg, use with quotes i.e.: "--analysis-mode fast"

lib/ArgumentParser.groovy

@@ -0,0 +1,61 @@
+/* Check arguments of a Nextflow function
+ *
+ * Nextflow script does not support the Groovy idiom:
+ *
+ *     def function(Map args[:], arg1, arg2, ...)
+ * 
+ * to support unordered kwargs. The methods here are designed
+ * to reduce boileplate while allowing Nextflow script to implement
+ *
+ *     def function(Map args[:])
+ *
+ * with required and default values. This is similar to some Python
+ * libraries' (notably matplotlib) extensive use of things like:
+ *
+ *     def function(*args, **kwargs)
+ *
+ * to implement generic APIs. Why do we want to do all this? Because
+ * we want to write library code with a clean set of required parameters
+ * but also extensible with non-required parameters with default values.
+ * This allows us to later add parameters without breaking existing code,
+ * and is very common practice elsewhere.
+ */
+
+import java.util.Set
+
+class ArgumentParser {
+    Set args
+    Map kwargs
+    String name
+
+    /* Parse arguments, raising an error on unknown keys */
+    public Map parse_args(LinkedHashMap given_args) {
+        Set opt_keys = kwargs.keySet()
+        Set given_keys = given_args.keySet()
+        check_required(given_keys)
+        check_unknown(given_keys, opt_keys)
+        return kwargs + given_args
+    }
+
+    /* Parse arguments, without raising an error for extra keys */
+    public Map parse_known_args(LinkedHashMap given_args) {
+        Set opt_keys = kwargs.keySet()
+        Set given_keys = given_args.keySet()
+        check_required(given_keys)
+        return kwargs + given_args
+    }
+
+    private void check_required(Set given) {
+        Set missing_keys = args - given
+        if (!missing_keys.isEmpty()) {
+            throw new Exception("Missing arguments for function ${name}: ${missing_keys}")
+        }
+    }
+
+    private void check_unknown(Set given, Set kwargs_keys) {
+        Set extra_keys = given - (args + kwargs_keys)
+        if (!extra_keys.isEmpty()) {
+            throw new Exception("Unknown arguments provided to function ${name}: ${extra_keys}.")
+        }
+    }
+}