Migrate from nf-val to nf-schema. Basic nf-test (real data)

EBI-Metagenomics · May 30, 2024 · 988ca49 · 988ca49
1 parent 1edc01b
commit 988ca49
Show file tree

Hide file tree

Showing 12 changed files with 99 additions and 54 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,36 @@
+name: nf-test CI
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+env:
+    NXF_ANSI_LOG: false
+    NFTEST_VER: "0.8.4"
+
+jobs:
+  test:
+    name: Run pipeline with test data
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+
+      - name: Run pipeline with test data
+        run: |
+          nf-test test
diff --git a/.gitignore b/.gitignore
@@ -12,3 +12,5 @@ results/
 .pytest_cache/
 
 assets/fetch_tool_credentials.json
+.nf-test.log
+.nf-test/
diff --git a/assets/mgnify_logo.png b/assets/mgnify_logo.png
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,16 +1,17 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/ebi-metagenomics/miassembler/" target="_blank">ebi-metagenomics/miassembler</a>
   analysis pipeline.
+
 report_section_order:
   "ebi-metagenomics-miassembler-methods-description":
     order: -1000
-  software_versions:
-    order: -1001
   "ebi-metagenomics-miassembler-summary":
     order: -1002
 
 export_plots: true
 
+skip_versions_section: true
+
 top_modules:
   - fastqc
   - quast

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
diff --git a/main.nf b/main.nf
@@ -15,7 +15,7 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp; paramsSummaryLog; paramsSummaryMap; } from 'plugin/nf-validation'
+include { validateParameters; paramsHelp; paramsSummaryLog; paramsSummaryMap; } from 'plugin/nf-schema'
 
 def summary_params = paramsSummaryMap(workflow)
 

diff --git a/nextflow.config b/nextflow.config
@@ -72,18 +72,18 @@ params {
     max_cpus                         = 32
     max_time                         = '168.h' // 7 days
 
-    // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
     // Assembler versions
     spades_version                   = "3.15.5"
     megahit_version                  = "1.2.9"
 
 }
 
+validation {
+    failUnrecognisedParams = true
+    lenientMode            = false
+    showHiddenParams       = false
+}
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -192,7 +192,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id 'nf-[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-[email protected]'
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/ebi-metagenomics/miassembler/master/nextflow_schema.json",
     "title": "ebi-metagenomics/miassembler pipeline parameters",
     "description": "Microbiome Informatics metagenomes assembly pipeline",
     "type": "object",
-    "definitions": {
+    "defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -241,47 +241,19 @@
                     "type": "string",
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
-                },
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Boolean whether to validate parameters against the schema at runtime",
-                    "default": true,
-                    "fa_icon": "fas fa-check-square",
-                    "hidden": true
-                },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                 }
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/defs/generic_options"
         }
     ]
 }
diff --git a/nf-test.config b/nf-test.config
@@ -0,0 +1,7 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test,docker"
+}
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -0,0 +1,25 @@
+nextflow_pipeline {
+
+    name "Test Workflow EBIMETAGENOMICS_MIASSEMBLER"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "tests/results"
+                bwamem2_reference_genomes_folder = "$projectDir/tests/human_phix/bwa2mem"
+                blast_reference_genomes_folder   = "$projectDir/tests/human_phix/blast"
+            }
+        }
+
+        then {
+            with(workflow) {
+                assert success
+                assert trace.tasks().size() == 19
+            }
+        }
+
+    }
+
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
diff --git a/workflows/miassembler.nf b/workflows/miassembler.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-schema'
 
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
@@ -21,7 +21,7 @@ log.info logo + paramsSummaryLog(workflow) + citation
 
 ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
 ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.fromPath("$projectDir/assets/mgnify_logo.png")
 ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 
 /*
@@ -50,11 +50,11 @@ include { ASSEMBLY_COVERAGE  } from '../subworkflows/local/assembly_coverage'
 //
 include { FASTQC as FASTQC_BEFORE      } from '../modules/nf-core/fastqc/main'
 include { FASTQC as FASTQC_AFTER       } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
-include { SPADES                      } from '../modules/nf-core/spades/main'
-include { MEGAHIT                     } from '../modules/nf-core/megahit/main'
-include { QUAST                       } from '../modules/nf-core/quast/main'
+include { MULTIQC                      } from '../modules/nf-core/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS  } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { SPADES                       } from '../modules/nf-core/spades/main'
+include { MEGAHIT                      } from '../modules/nf-core/megahit/main'
+include { QUAST                        } from '../modules/nf-core/quast/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -149,7 +149,7 @@ workflow MIASSEMBLER {
 
     SPADES(
         qc_reads.xspades.map { meta, reads -> [meta, reads, [], []] },
-        params.assembler,
+        params.assembler ?: "metaspades",
         [], // yml input parameters, which we don't use
         []  // hmm, not used
     )