diff --git a/CHANGELOG.md b/CHANGELOG.md
index 530200b..25bd82f 100644
--- a/CHANGELOG.md
+++ b/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`
diff --git a/CITATIONS.md b/CITATIONS.md
index 208cfa1..e1811c7 100644
--- a/CITATIONS.md
+++ b/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].
diff --git a/README.md b/README.md
index 6cf36dc..6f25df4 100644
--- a/README.md
+++ b/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
 
diff --git a/conf/modules.config b/conf/modules.config
index 4a653ed..4e4f33f 100644
--- a/conf/modules.config
+++ b/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'
     }
diff --git a/modules.json b/modules.json
index 28c9108..91d03f9 100644
--- a/modules.json
+++ b/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",
diff --git a/modules/nf-core/fq/lint/environment.yml b/modules/nf-core/fq/lint/environment.yml
new file mode 100644
index 0000000..74b1460
--- /dev/null
+++ b/modules/nf-core/fq/lint/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fq=0.12.0
diff --git a/modules/nf-core/fq/lint/main.nf b/modules/nf-core/fq/lint/main.nf
new file mode 100644
index 0000000..943314c
--- /dev/null
+++ b/modules/nf-core/fq/lint/main.nf
@@ -0,0 +1,33 @@
+process FQ_LINT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fq:0.12.0--h9ee0642_0':
+        'biocontainers/fq:0.12.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.fq_lint.txt"), emit: lint
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    fq lint \\
+        $args \\
+        $fastq > ${prefix}.fq_lint.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fq: \$(echo \$(fq lint --version | sed 's/fq-lint //g'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fq/lint/meta.yml b/modules/nf-core/fq/lint/meta.yml
new file mode 100644
index 0000000..7240fb5
--- /dev/null
+++ b/modules/nf-core/fq/lint/meta.yml
@@ -0,0 +1,43 @@
+name: "fq_lint"
+description: fq lint is a FASTQ file pair validator.
+keywords:
+  - lint
+  - fastq
+  - validate
+tools:
+  - "fq":
+      description: "fq is a library to generate and validate FASTQ file pairs."
+      homepage: "https://github.com/stjude-rust-labs/fq"
+      documentation: "https://github.com/stjude-rust-labs/fq"
+      tool_dev_url: "https://github.com/stjude-rust-labs/fq"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fastq:
+        type: file
+        description: FASTQ file list
+        pattern: "*.fastq{,.gz}"
+output:
+  - lint:
+      - meta:
+          type: file
+          description: Lint output
+          pattern: "*.fq_lint.txt"
+      - "*.fq_lint.txt":
+          type: file
+          description: Lint output
+          pattern: "*.fq_lint.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
diff --git a/modules/nf-core/fq/lint/tests/main.nf.test b/modules/nf-core/fq/lint/tests/main.nf.test
new file mode 100644
index 0000000..ec2eaf8
--- /dev/null
+++ b/modules/nf-core/fq/lint/tests/main.nf.test
@@ -0,0 +1,63 @@
+nextflow_process {
+
+    name "Test Process FQ_LINT"
+    script "../main.nf"
+    process "FQ_LINT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fq"
+    tag "fq/lint"
+
+    test("test_fq_lint_success") {
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                             [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                               file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                           ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.lint.get(0).get(1) ==~ ".*/test.fq_lint.txt" },
+                { assert path(process.out.lint.get(0).get(1)).getText().contains("fq-lint start") },
+                { assert path(process.out.lint.get(0).get(1)).getText().contains("read 100 records") },
+                { assert path(process.out.lint.get(0).get(1)).getText().contains("fq-lint end") },
+            )
+        }
+
+    }
+
+    test("test_fq_lint_fail") {
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                             [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                               file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                           ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert !process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fq/lint/tests/main.nf.test.snap b/modules/nf-core/fq/lint/tests/main.nf.test.snap
new file mode 100644
index 0000000..fec8e52
--- /dev/null
+++ b/modules/nf-core/fq/lint/tests/main.nf.test.snap
@@ -0,0 +1,25 @@
+{
+    "test_fq_lint_fail": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "lint": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-19T16:37:02.133847389"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fq/lint/tests/tags.yml b/modules/nf-core/fq/lint/tests/tags.yml
new file mode 100644
index 0000000..9c9c323
--- /dev/null
+++ b/modules/nf-core/fq/lint/tests/tags.yml
@@ -0,0 +1,2 @@
+fq/lint:
+  - modules/nf-core/fq/lint/**
diff --git a/nextflow.config b/nextflow.config
index bb1cb27..a220f59 100644
--- a/nextflow.config
+++ b/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
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 248660b..e5760c7 100644
--- a/nextflow_schema.json
+++ b/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"
         },
diff --git a/tests/rnaseq.main.nf.test b/tests/rnaseq.main.nf.test
new file mode 100644
index 0000000..9225dd5
--- /dev/null
+++ b/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")
+                    )
+                },
+            )
+        }
+    }
+}
diff --git a/tests/rnaseq.main.nf.test.config b/tests/rnaseq.main.nf.test.config
new file mode 100644
index 0000000..f85acb5
--- /dev/null
+++ b/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'
+
+}
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 9488cea..69fc29b 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -7,6 +7,7 @@ include { samplesheetToList } from 'plugin/nf-schema'
 */
 
 include { SEQTK_SAMPLE                  } from '../modules/nf-core/seqtk/sample/main'
+include { FQ_LINT                       } from '../modules/nf-core/fq/lint/main'
 include { FASTQC                        } from '../modules/nf-core/fastqc/main'
 include { SEQFU_STATS                   } from '../modules/nf-core/seqfu/stats'
 include { FASTQSCREEN_FASTQSCREEN       } from '../modules/nf-core/fastqscreen/fastqscreen/main'
@@ -38,6 +39,24 @@ workflow SEQINSPECTOR {
     ch_multiqc_extra_files = Channel.empty()
     ch_multiqc_reports     = Channel.empty()
 
+    //
+    // MODULE: Run FQ_LINT to catch early errors
+    //
+    if ( !("fq" in skip_tools) ) {
+        FQ_LINT (
+            ch_samplesheet
+        )
+        ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
+        // This catches all FASTQs that pass linting
+        // If you use an error strategy that allows FQ_LINT to fail,
+        // only valid FASTQ files will be passed to the next module
+        ch_samplesheet = FQ_LINT.out.lint
+                            .join(ch_samplesheet)
+                            .map { meta, fq_lint, reads ->
+                                [meta, reads]
+                            }
+    }
+
     //
     // MODULE: Run Seqtk sample to perform subsampling
     //