Adds fq/lint for early validation of FASTQs

CHANGELOG.md

@@ -19,6 +19,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
+- [#67](https://github.com/nf-core/seqinspector/pull/67) Add FASTQ linting for early validation
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 
 ### `Fixed`

CITATIONS.md

@@ -10,6 +10,8 @@
 
 ## Pipeline tools
 
+- [FQ](https://github.com/stjude-rust-labs/fq)
+
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

README.md

@@ -31,9 +31,10 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
+1. Lint FASTQs with ([`fq`](https://github.com/stjude-rust-labs/fq))
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
-2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

conf/modules.config

@@ -18,6 +18,15 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: 'FQ_LINT' {
+        ext.args      = { params.fq_lint_args }
+        errorStrategy = {
+                            task.exitStatus in ((130..145) + 104) ? 'retry'  :
+                            params.continue_with_lint_fail        ? 'ignore' :
+                            'finish'
+                        }
+    }
+
     withName: SEQTK_SAMPLE {
         ext.args = '-s100'
     }

modules.json

@@ -26,6 +26,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",

nextflow.config

@@ -13,7 +13,12 @@ params {
     // Input options
     input                      = null
     sample_size                = 0
+
+    // Options
+    fq_lint_args               = ""
+    continue_with_lint_fail    = false
     skip_tools                 = ''
+
     // References
     genome                     = null
     fasta                      = null

nextflow_schema.json

@@ -31,7 +31,6 @@
                 },
                 "outdir": {
                     "type": "string",
-                    "default": null,
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
@@ -51,7 +50,25 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip",
-                    "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample)?,?)*(?<!,)$"
+                    "pattern": "^((fq|fastqc|fastqscreen|seqfu_stats|seqtk_sample)?,?)*(?<!,)$"
+                }
+            }
+        },
+        "validation_options": {
+            "title": "Validation options",
+            "type": "object",
+            "description": "Options for validating and screening FASTQ files.",
+            "default": "",
+            "properties": {
+                "fq_lint_args": {
+                    "type": "string",
+                    "description": "Arguments to pass to FQ lint",
+                    "help_text": "Arguments to pass to FQ lint. This can be used to disable overly strict linting. See https://github.com/stjude-rust-labs/fq?tab=readme-ov-file#lint for more information."
+                },
+                "continue_with_lint_fail": {
+                    "type": "boolean",
+                    "description": "Whether to continue with the pipeline if linting fails for a single sample.",
+                    "help_text": "If set to true, the pipeline will continue with the remaining samples if linting fails for a single sample. If set to false, the pipeline will terminate if linting fails for a single sample."
                 }
             }
         },
@@ -250,6 +267,9 @@
         {
             "$ref": "#/$defs/input_output_options"
         },
+        {
+            "$ref": "#/$defs/validation_options"
+        },
         {
             "$ref": "#/$defs/reference_genome_options"
         },

tests/rnaseq.main.nf.test

@@ -0,0 +1,87 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf on NovaSeq6000 data"
+    script "../main.nf"
+    tag "seqinspector"
+    tag "PIPELINE"
+
+    test("rnaseq data test fail linting") {
+
+        when {
+            config "./rnaseq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                // Linting should fail!
+                { assert workflow.failed }
+            )
+        }
+    }
+
+    test("rnaseq data test skip linting") {
+
+        when {
+            config "./rnaseq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                skip_tools = "fq"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("rnaseq data test ignore linting") {
+
+        when {
+            config "./rnaseq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                continue_with_lint_fail = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt")
+                    )
+                },
+            )
+        }
+    }
+
+    test("rnaseq data test add args to fq/lint") {
+
+        when {
+            config "./rnaseq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                fq_lint_args = "--disable-validator P001"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
+                        path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt")
+                    )
+                },
+            )
+        }
+    }
+}

tests/rnaseq.main.nf.test.config

@@ -0,0 +1,8 @@
+// Load the basic test config
+includeConfig 'nextflow.config'
+
+// Load the correct samplesheet for that test
+params {
+    input  = params.pipelines_testdata_base_path + '626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv'
+
+}