Made the hic param pattern more flexible

.github/workflows/ci.yml

@@ -30,10 +30,11 @@ jobs:
           - invalid
           - stub
           - noltr
+          - hicparam
         include:
           - OPTION_STUB: ""
           - OPTION_STUB: "-stub"
-            TEST_PARAMS: stub
+            TEST_PARAMS: [stub, hicparam]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -55,3 +56,31 @@ jobs:
             -params-file \
             ./tests/${{ matrix.TEST_PARAMS }}/params.json \
             ${{ matrix.OPTION_STUB }}
+
+  nf-test:
+    name: Run nf-tests
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/assemblyqc') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ matrix.NXF_VER }}
+
+      - name: Install nf-test
+        uses: nf-core/[email protected]
+
+      - name: Run nf-tests
+        run: |
+          nf-test \
+            test \
+            --verbose \
+            tests

.gitignore

@@ -10,3 +10,7 @@ testing*
 # PFR files
 *.stdout
 *.stderr
+
+# nf-test files
+.nf-test/
+.nf-test.log

CHANGELOG.md

@@ -3,6 +3,21 @@
 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).
 
+## v2.1.1+dev - [19-Sep-2024]
+
+### `Added`
+
+1. Configured nf-test for function testing
+
+### `Fixed`
+
+1. Made the `hic` param pattern more flexible as `^SR\w+$|^\S+\{1,2\}[\w\.]*\.f(ast)?q\.gz$`
+
+### `Dependencies`
+
+1. Nextflow!>=23.04.0
+2. [email protected]
+
 ## v2.1.0 - [31-July-2024]
 
 ### `Added`

CITATION.cff

@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.1.0
+version: 2.1.1+dev
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477

cleanNXF.sh

@@ -9,3 +9,7 @@ do
     rm -rf "work/$i"
 done
 echo "Cleaned work..."
+
+rm -f .nf-test.log
+rm -rf .nf-test
+echo "Cleaned nf-test..."

docs/parameters.md

@@ -66,12 +66,12 @@ A Nextflow pipeline which evaluates assembly quality with multiple QC tools and
 
 ## HiC options
 
-| Parameter            | Description                                                                            | Type      | Default                                           | Required | Hidden |
-| -------------------- | -------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
-| `hic`                | HiC reads path provided as a SRA ID or as paired reads with pattern '\*{1,2}.fastq.gz' | `string`  |                                                   |          |        |
-| `hic_skip_fastp`     | Skip HiC read trimming                                                                 | `boolean` |                                                   |          |        |
-| `hic_skip_fastqc`    | Skip HiC read QC                                                                       | `boolean` |                                                   |          |        |
-| `hic_fastp_ext_args` | Additional parameters for fastp trimming                                               | `string`  | --qualified_quality_phred 20 --length_required 50 |          |        |
+| Parameter            | Description                                                                              | Type      | Default                                           | Required | Hidden |
+| -------------------- | ---------------------------------------------------------------------------------------- | --------- | ------------------------------------------------- | -------- | ------ |
+| `hic`                | HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz' | `string`  |                                                   |          |        |
+| `hic_skip_fastp`     | Skip HiC read trimming                                                                   | `boolean` |                                                   |          |        |
+| `hic_skip_fastqc`    | Skip HiC read QC                                                                         | `boolean` |                                                   |          |        |
+| `hic_fastp_ext_args` | Additional parameters for fastp trimming                                                 | `string`  | --qualified_quality_phred 20 --length_required 50 |          |        |
 
 ## Synteny options
 

docs/usage.md

@@ -90,7 +90,7 @@ This section provides additional information for parameters. It does not list al
 
 ### HiC
 
-- `hic`: Path to reads provided as a SRA ID or as a path to paired reads with pattern '\*{1,2}.(fastq|fq).gz'. These reads are applied to each assembly listed by `input`.
+- `hic`: Path to reads provided as a SRA ID or as a path to paired reads such as 'hic_reads{1,2}.fastq.gz'. These reads are applied to each assembly listed by `input`.
 
 ### Synteny analysis
 

nextflow.config

@@ -283,7 +283,7 @@ manifest {
     description     = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.0'
+    version         = '2.1.1+dev'
     doi             = 'https://doi.org/10.1093/bioinformatics/btae477'
 }
 

nextflow_schema.json

@@ -213,8 +213,8 @@
             "properties": {
                 "hic": {
                     "type": "string",
-                    "description": "HiC reads path provided as a SRA ID or as paired reads with pattern '*{1,2}.fastq.gz'",
-                    "pattern": "^SR\\w+$|^\\S+\\{1,2\\}\\.f(ast)?q\\.gz$"
+                    "description": "HiC reads path provided as a SRA ID or as paired reads such as 'hic_reads{1,2}.fastq.gz'",
+                    "pattern": "^SR\\w+$|^\\S+\\{1,2\\}[\\w\\.]*\\.f(ast)?q\\.gz$"
                 },
                 "hic_skip_fastp": {
                     "type": "boolean",

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "nextflow.config"
+    profile ""
+
+}

tests/hicparam/assemblysheet.csv

@@ -0,0 +1,2 @@
+tag,fasta
+test,tests/hicparam/test_genome.fa.gz

tests/hicparam/hicparam.nf

@@ -0,0 +1,10 @@
+import groovy.json.JsonSlurper
+
+def checkHiCParam(paramValue, schema) {
+    def jsonSlurper = new JsonSlurper()
+    def jsonContent = jsonSlurper.parse ( file ( schema, checkIfExists: true ) )
+    def pattern = jsonContent.definitions.hic_options.properties.hic.pattern
+    def match = paramValue ==~ pattern
+
+    return match
+}

tests/hicparam/hicparam.nf.test

@@ -0,0 +1,118 @@
+nextflow_function {
+
+    name "checkHiCParam"
+    script "./hicparam.nf"
+    function "checkHiCParam"
+
+    test("Dummy_hic.R{1,2}.fq.gz") {
+        when {
+            function {
+                """
+                input[0] = "Dummy_hic.R{1,2}.fq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("Dummy_hic.{1,2}.fq.gz") {
+        when {
+            function {
+                """
+                input[0] = "Dummy_hic.{1,2}.fq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("Dummy_hic{1,2}.fastq.gz") {
+        when {
+            function {
+                """
+                input[0] = "Dummy_hic{1,2}.fastq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("Dummy_hic.R{1,2}.merged.fq.gz") {
+        when {
+            function {
+                """
+                input[0] = "Dummy_hic.R{1,2}.merged.fq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("Dummy_hic{1,2}_merged.samtools._check.fq.gz") {
+        when {
+            function {
+                """
+                input[0] = "Dummy_hic{1,2}_merged.samtools._check.fq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("CK13_02_hic_R{1,2}.merged.fastq.gz") {
+        when {
+            function {
+                """
+                input[0] = "CK13_02_hic_R{1,2}.merged.fastq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("CK13_02_hic_1.merged.fastq.gz -- fail") {
+        when {
+            function {
+                """
+                input[0] = "CK13_02_hic_1.merged.fastq.gz"
+                input[1] = "$baseDir/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert ! function.result
+        }
+    }
+}

tests/hicparam/params.json

@@ -0,0 +1,9 @@
+{
+    "config_profile_name": "Test to verify hic param validation",
+    "config_profile_description": "Test to verify hic param validation",
+    "input": "tests/hicparam/assemblysheet.csv",
+    "hic": "tests/hicparam/hic/Dummy_hic_{1,2}.merged.fq.gz",
+    "max_cpus": 2,
+    "max_memory": "6.GB",
+    "max_time": "6.h"
+}