Merge branch 'CW-790' into 'dev'

template updates

Closes CW-790

See merge request epi2melabs/workflow-containers/wf-isoforms!57

.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.

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).
 
+## [v0.1.4]
+### Changed
+- Args parser for fastqingress
+- Set out_dir option type to ensure output is written to correct directory on Windows
+
 ## [v0.1.3]
 ### Changed
 - Better help text on cli

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}.")
+        }
+    }
+}

lib/fastqingress.nf

@@ -1,5 +1,7 @@
+import ArgumentParser
+
 process handleSingleFile {
-    label "isoforms"
+    label params.process_label
     cpus 1
     input:
         file reads
@@ -16,7 +18,7 @@ process handleSingleFile {
 
 
 process checkSampleSheet {
-    label "isoforms"
+    label params.process_label
     cpus 1
     input:
         file "sample_sheet.txt"
@@ -73,7 +75,7 @@ def find_fastq(pattern, maxdepth)
  * @param input_folder Top-level input directory.
  * @param staging Top-level output_directory.
  * @return A File object representating the staging directory created
- *     under output_folder
+ *     under output
  */ 
 def sanitize_fastq(input_folder, staging)
 {
@@ -111,8 +113,8 @@ def sanitize_fastq(input_folder, staging)
  */
 def get_subdirectories(input_directory)
 {
-    barcode_dirs = file("$input_directory/barcode*", type: 'dir', maxdepth: 1)
+    barcode_dirs = file(input_directory.resolve("barcode*"), type: 'dir', maxdepth: 1)
-    all_dirs = file("$input_directory/*", type: 'dir', maxdepth: 1)
+    all_dirs = file(input_directory.resolve("*"), type: 'dir', maxdepth: 1)
     non_barcoded = ( all_dirs + barcode_dirs ) - all_dirs.intersect(barcode_dirs)
     return [barcode_dirs, non_barcoded]
 }
@@ -223,9 +225,11 @@ def handle_flat_dir(input_directory, sample_name)
  * @param barcoded_dirs List of barcoded directories (barcodeXX,...)
  * @param sample_sheet List of tuples mapping barcode to sample name
  *     or a simple string for non-multiplexed data.
+ * @param min_barcode Minimum barcode to accept.
+ * @param max_barcode Maximum (inclusive) barcode to accept.
  * @return Channel of tuples (path, sample_id, type)
  */
-def handle_barcoded_dirs(barcoded_dirs, sample_sheet)
+def handle_barcoded_dirs(barcoded_dirs, sample_sheet, min_barcode, max_barcode)
 {
     valid_dirs = get_valid_directories(barcoded_dirs)
     // link sample names to barcode through sample sheet
@@ -233,17 +237,36 @@ def handle_barcoded_dirs(barcoded_dirs, sample_sheet)
         sample_sheet = Channel
             .fromPath(valid_dirs)
             .filter(~/.*barcode[0-9]{1,3}$/)  // up to 192
+            .filter { barcode_in_range(it, min_barcode, max_barcode) }
             .map { path -> tuple(path.baseName, path.baseName, 'test_sample') }
     }
     return Channel
         .fromPath(valid_dirs)
         .filter(~/.*barcode[0-9]{1,3}$/)  // up to 192
+        .filter { barcode_in_range(it, min_barcode, max_barcode) }
         .map { path -> tuple(path.baseName, path) }
         .join(sample_sheet)
         .map { barcode, path, sample, type -> tuple(path, sample, type) }
 }
 
 
+/**
+ * Determine if a barcode path is within a required numeric range
+ *
+ * @param path barcoded directory (barcodeXX).
+ * @param min_barcode Minimum barcode to accept.
+ * @param max_barcode Maximum (inclusive) barcode to accept.
+ */
+def barcode_in_range(path, min_barcode, max_barcode)
+{
+    pattern = ~/barcode(\d+)/
+    matcher = "${path}" =~ pattern
+    value = matcher[0][1].toInteger()
+    valid = ((value >= min_barcode) && (value <= max_barcode))
+    return valid
+}
+
+
 /**
  * Take a list of non-barcode directories to return a channel 
  * of named samples. Samples are named by directory baseName.
@@ -264,33 +287,49 @@ def handle_non_barcoded_dirs(non_barcoded_dirs)
  * Take an input (file or directory) and return a channel of
  * named samples.
  *
- *
  * @param input Top level input file or folder to locate fastq data.
  * @param sample string to name single sample data.
  * @param sample_sheet Path to sample sheet CSV file.
+ * @param sanitize regularize inputs from EPI2ME platform.
+ * @param output output location, required if sanitize==true
+ * @param min_barcode Minimum barcode to accept.
+ * @param max_barcode Maximum (inclusive) barcode to accept.
+ *
  * @return Channel of tuples (path, sample_id, type)
  */
-def fastq_ingress(input, output_folder, sample, sample_sheet, sanitize)
+def fastq_ingress(Map arguments)
 {
+    def parser = new ArgumentParser(
+        args:["input"],
+        kwargs:[
+            "sample":null, "sample_sheet":null, "sanitize":false, "output":null,
+            "min_barcode":0, "max_barcode":Integer.MAX_VALUE],
+        name:"fastq_ingress")
+    Map margs = parser.parse_args(arguments)
+    
+    if (margs.sanitize && margs.output == null) {
+        throw new Exception("Argument 'output' required if 'sanitize' is true.")
+    }
+
     println("Checking fastq input.")
-    input = file(input);
+    input = file(margs.input)
 
     // Handle file input
     if (input.isFile()) {
         // Assume sample is a string at this point
         println('Single file input detected.')
-        if (sample_sheet) {
+        if (margs.sample_sheet) {
             println('Warning: `--sample_sheet` given but single file input found. Ignoring.')
         }
-        return handle_single_file(input, sample)
+        return handle_single_file(input, margs.sample)
     }
 
     // Handle directory input
     if (input.isDirectory()) {
         // EPI2ME harness 
-        if (sanitize) {
+        if (margs.sanitize) {
-            staging = file(output_folder).resolve("staging")
+            staging = file(margs.output).resolve("staging")
-            input = sanitize_fastq(file(input), staging)
+            input = sanitize_fastq(input, staging)
         }
 
         // Get barcoded and non barcoded subdirectories
@@ -299,13 +338,13 @@ def fastq_ingress(input, output_folder, sample, sample_sheet, sanitize)
         // Case 03: If no subdirectories, handle the single dir
         if (!barcoded && !non_barcoded) {
             println("Single directory input detected.")
-            if (sample_sheet) {
+            if (margs.sample_sheet) {
                 println('Warning: `--sample_sheet` given but single non-barcode directory found. Ignoring.')
             }
-            return handle_flat_dir(input, sample)
+            return handle_flat_dir(input, margs.sample)
         }
 
-        if (sample) {
+        if (margs.sample) {
             println('Warning: `--sample` given but multiple directories found, ignoring.')
         }
 
@@ -314,16 +353,17 @@ def fastq_ingress(input, output_folder, sample, sample_sheet, sanitize)
         barcoded_samples = Channel.empty()
         if (barcoded) {
             println("Barcoded directories detected.")
-            if (sample_sheet) {
+            sample_sheet = null
-                sample_sheet = get_sample_sheet(sample_sheet)
+            if (margs.sample_sheet) {
+                sample_sheet = get_sample_sheet(margs.sample_sheet)
             }
-            barcoded_samples = handle_barcoded_dirs(barcoded, sample_sheet)
+            barcoded_samples = handle_barcoded_dirs(barcoded, sample_sheet, margs.min_barcode, margs.max_barcode)
         }
 
         non_barcoded_samples = Channel.empty()
         if (non_barcoded) {
             println("Non barcoded directories detected.")
-            if (!barcoded && sample_sheet) {
+            if (!barcoded && margs.sample_sheet) {
                 println('Warning: `--sample_sheet` given but no barcode directories found.')
             }
             non_barcoded_samples = handle_non_barcoded_dirs(non_barcoded)

main.nf

@@ -502,9 +502,12 @@ workflow {
         ref_annotation = file("$projectDir/data/OPTIONAL_FILE")
     }
 
-    reads = fastq_ingress(
+    reads = fastq_ingress([
-        params.fastq, params.out_dir, params.sample, params.sample_sheet, params.sanitize_fastq
+        "input":params.fastq,
-    )
+        "sample":params.sample,
+        "sample_sheet":params.sample_sheet,
+        "sanitize": params.sanitize_fastq,
+        "output":params.out_dir])
 
     pipeline(reads, ref_genome, ref_annotation)
 

nextflow.config

@@ -23,15 +23,16 @@ params {
     sample = null
     sample_sheet = null
     sanitize_fastq = false
-    wfversion = "v0.1.3"
+    wfversion = "v0.1.4"
     aws_image_prefix = null
     aws_queue = null
     report_name = "report"
+    process_label = "isoforms"
 
     monochrome_logs = false
     validate_params = true
     show_hidden_params = false
-    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion,wf'
+    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion,wf,process_label'
 
     // Process cDNA reads using pychopper, turn off for direct RNA:
     direct_rna = false

nextflow_schema.json

@@ -15,6 +15,7 @@
                 "out_dir": {
                     "type": "string",
                     "default": "output",
+                    "format": "path",
                     "description": "Directory for output of all user-facing files."
                 },
                 "fastq": {
@@ -280,7 +281,7 @@
         },
         "wfversion": {
             "type": "string",
-            "default": "v0.1.3",
+            "default": "v0.1.4",
             "hidden": true
         },
         "monochrome_logs": {