diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12fc64ce..597cb56f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,11 +8,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#109](https://github.com/nf-core/seqinspector/pull/109) Adds ToulligQC module for long read QC
-- [#204](https://github.com/nf-core/seqinspector/pull/204) Added Fastp module
 - [#202](https://github.com/nf-core/seqinspector/pull/202) Added support for fasta fai file as input (via params or igenomes) for the pipeline
+- [#204](https://github.com/nf-core/seqinspector/pull/204) Added Fastp module
 - [#206](https://github.com/nf-core/seqinspector/pull/206) Added FASTQE for more comprehensive QC of FASTQ files
 - [#208](https://github.com/nf-core/seqinspector/pull/208) Add FASTQ linting for early validation with FQ/LINT
 - [#210](https://github.com/nf-core/seqinspector/pull/210) Added kraken2 subworkflow
+- [#212](https://github.com/nf-core/seqinspector/pull/212) Add CheckQC module
 
 ### `Fixed`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index 3cd7d601..1862fd85 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,6 +14,10 @@
 
   > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE; 2019:314-324. doi:10.1109/IPDPS.2019.00041
 
+- [checkQC](https://github.com/Molmed/checkQC)
+
+  > Åslin et al., (2018). CheckQC: Quick quality control of Illumina sequencing runs. Journal of Open Source Software, 3(22), 556, https://doi.org/10.21105/joss.00556
+
 - [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 700f7db8..1527a4b0 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | `Trimming`                 | [`Fastp`](https://github.com/OpenGene/fastp)                                                                        | Trimming of reads. Only performs trimming if `--tools` parameter is given.                    | [RNA, DNA, synthetic]   | [N/A]                                                                                   | no           |
 | `Indexing, Mapping`        | [`Bwamem2`](https://github.com/bwa-mem2/bwa-mem2)                                                                   | Align reads to reference                                                                      | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `Indexing`                 | [`SAMtools`](http://github.com/samtools)                                                                            | Index aligned BAM files, create FASTA index                                                   | [DNA]                   | [N/A]                                                                                   | yes          |
+| `QC`                       | [`checkQC`](https://github.com/Molmed/checkQC)                                                                      | Read QC                                                                                       | [RNA, DNA]              | Illumina rundir                                                                         | no           |
 | `QC`                       | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                       | [`FASTQE`](https://fastqe.com/)                                                                                     | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
 | `QC`                       | [`FastqScreen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)                                   | Basic contamination detection                                                                 | [RNA, DNA]              | [N/A]                                                                                   | yes          |
@@ -60,6 +61,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | Tool        | Version |
 | ----------- | ------- |
 | bwamem2     | 2.3     |
+| checkQC     | 4.1.0   |
 | fq/lint     | 0.12.0  |
 | fastp       | 1.1.0   |
 | fastqc      | 0.12.1  |
diff --git a/assets/checkqc_config.yml b/assets/checkqc_config.yml
new file mode 100644
index 00000000..7831ec71
--- /dev/null
+++ b/assets/checkqc_config.yml
@@ -0,0 +1,791 @@
+# For information about config usage, see http://checkqc.readthedocs.io/en/latest/#configuration-file
+
+# Use this section to provide configuration options to the parsers
+parser_configurations:
+  StatsJsonParser:
+    # Path to where the bcl2fastq output (i.e. fastq files, etc) is located relative to
+    # the runfolder
+    bcl2fastq_output_path: Data/Intensities/BaseCalls
+  SamplesheetParser:
+    samplesheet_name: SampleSheet.csv
+  from_bclconvert:
+    reports_location: Reports
+
+default_view: illumina_data_view
+
+default_handlers:
+  - name: UndeterminedPercentageHandler
+    warning: unknown
+    error: 9 # <% Phix on lane> + < value as %>
+  - name: UnidentifiedIndexHandler
+    significance_threshold: 1 # % of reads in unidentified
+    # Indexes which are white-listed will only cause a warning even if they occur
+    # above the significance level.
+    # They will be matched like regular expressions,
+    # so e.g. NNN will match exactly three NNNs, while
+    # N{3,} will match three or more Ns.
+    white_listed_indexes:
+      - .*N.*
+      - G{6,}
+
+hiseq2500_rapidhighoutput_v4:
+  51-71:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 180 # Millons of clusters
+        error: unknown
+      - name: Q30Handler
+        warning: 85 # Give percentage for reads greater than Q30
+        error: unknown # Give percentage for reads greater than Q30
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 135 # 75 % of threshold for clusters pass filter
+    view: illumina_data_view
+  100-111:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 180
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 135
+  121-131:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 180
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 135
+
+hiseq2500_rapidrun_v2:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 110
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 82.5
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 110
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 82.5
+  251:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 110
+        error: unknown
+      - name: Q30Handler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: unknown
+        error: 5
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 82.5
+
+hiseqx_v2:
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 400
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 300
+
+novaseq_SP:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 325
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 243.75
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 325
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 243.75
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 325
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 243.75
+  251:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 325
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 243.75
+
+novaseq_S1:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 650
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 487.5
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 650
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 487.5
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 650
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 487.5
+
+novaseq_S2:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1650
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 1237.5
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1650
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 1237.5
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1650
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 1237.5
+
+novaseq_S4:
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 2000
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 1500
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 2000
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 1500
+
+novaseqxplus_1.5B:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 800
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 600
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 800
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 600
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 800
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 600
+
+novaseqxplus_10B:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1250
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 937.5
+  101:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1250
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 937.5
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1250
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 937.5
+
+novaseqxplus_25B:
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 3250
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 2437.5
+
+miseq_nano_v2:
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+  251:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 1
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+
+miseq_micro_v2:
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 4
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+
+miseq_v2:
+  51:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 10
+        error: unknown
+      - name: Q30Handler
+        warning: 90
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 10
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+  251:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 10
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 7.5
+
+miseq_v3:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 18
+        error: unknown
+      - name: Q30Handler
+        warning: 85
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 13.5
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 18
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 2
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 13.5
+  301:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 18
+        error: unknown
+      - name: Q30Handler
+        warning: 70
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 13.5
+      - name: UndeterminedPercentageHandler
+        warning: unknown
+        error: 14 # <% Phix on lane> + < value as %>
+
+iseq_v1:
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 4
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 5
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 3
+
+nextseq500_high:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 100
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 100
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  301:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 60
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 15
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+
+nextseq500_mid:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  301:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+
+nextseq550_high:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 100
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 100
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  301:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 100
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 75
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+
+nextseq550_mid:
+  76:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 80
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  151:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
+  301:
+    handlers:
+      - name: ClusterPFHandler
+        warning: 32
+        error: unknown
+      - name: Q30Handler
+        warning: 75
+        error: unknown
+      - name: ReadsPerSampleHandler
+        warning: unknown
+        error: 24
+      - name: ErrorRateHandler
+        allow_missing_error_rate: False
+        warning: 1.5
+        error: unknown
diff --git a/conf/modules.config b/conf/modules.config
index da9ea722..6bf4a705 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -50,7 +50,11 @@ process {
         ]
     }
 
-    withName: 'TOULLIGQC' {
+    withName: CHECKQC {
+        tag = { "${run_dir.simpleName}" }
+    }
+
+    withName: TOULLIGQC {
         ext.args = ''
         publishDir = [[
             path: { "${params.outdir}/toulligqc" },
diff --git a/conf/test.config b/conf/test.config
index a924ce3d..3b0013cd 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -28,4 +28,8 @@ process {
         memory: '8.GB',
         time: '1.h'
     ]
+
+    withName: CHECKQC {
+        ext.args = '--use-closest-read-length'
+    }
 }
diff --git a/docs/output.md b/docs/output.md
index 08b53d4c..3160aa00 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -13,6 +13,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
 - [FASTQE](#fastqe) - Raw read QC
+- [CheckQC](#checkqc) - QC of an Illumina run
 - [Kraken2](#kraken2) - Phylogenetic assignment of reads using k-mers
 - [Krona](#krona) - Interactive visualization of Kraken2 results
 - [SeqFu Stats](#seqfu-stats) - Statistics for FASTA or FASTQ files
@@ -50,6 +51,16 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and can generat
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### CheckQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `checkqc/`
+  - `checkqc_report.json`: Reports sequencing metrics that are not fulfilled. Note that the CheckQC module in MultiQC currently does not support BCL Convert data, so if the report if based on data from that demultiplexer it will not be visualized in the MutliQC report. Results can be found in the output directory.
+
+</details>
+
 ### Kraken2
 
 [Kraken](https://ccb.jhu.edu/software/kraken2/) is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps -mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.
diff --git a/docs/usage.md b/docs/usage.md
index 81136142..0f1bbbbe 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -168,7 +168,8 @@ It is possible to also chose bundles of pre-specified tools using the `tools_bun
 
 Currently, the following bundles are available:
 
-:::info{title="default"}{collapse}
+<details>
+<summary>default</summary>
 
 Requirements:
 
@@ -183,9 +184,10 @@ Tools:
 - rundirparser
 - seqfu_stats
 
-:::
+</details>
 
-:::info{title="all"}{collapse}
+<details>
+<summary>all</summary>
 
 Requirements:
 
@@ -194,6 +196,7 @@ Requirements:
 
 Tools:
 
+- checkQC
 - fastqc
 - fastqscreen
 - picard_collecthsmetrics
@@ -202,9 +205,10 @@ Tools:
 - seqfu_stats
 - toulligqc
 
-:::
+</details>
 
-:::info{title="minimal"}{collapse}
+<details>
+<summary>minimal</summary>
 
 Requirements:
 
@@ -216,10 +220,10 @@ Tools:
 - fastqscreen
 - picard_collectmultiplemetrics
 - seqfu_stats
+</details>
 
-:::
-
-:::info{title="bam"}{collapse}
+<details>
+<summary>bam</summary>
 
 Requirements:
 
@@ -230,18 +234,20 @@ Tools:
 - picard_collecthsmetrics
 - picard_collectmultiplemetrics
 
-:::
+</details>
 
-:::info{title="fastq"}{collapse}
+<details>
+<summary>fastq</summary>
 
 Tools:
 
 - fastqc
 - fastqscreen
 
-:::
+</details>
 
-:::info{title="illumina"}{collapse}
+<details>
+<summary>illumina</summary>
 
 Requirements:
 
@@ -249,12 +255,13 @@ Requirements:
 
 Tools:
 
+- checkQC
 - rundirparser
 - seqfu_stats
+</details>
 
-:::
-
-:::info{title="ont"}{collapse}
+<details>
+<summary>ont</summary>
 
 Tools:
 
@@ -263,7 +270,7 @@ Tools:
 - seqfu_stats
 - toulligqc
 
-:::
+</details>
 
 ### Available functionality and tools
 
diff --git a/main.nf b/main.nf
index 2fb26f43..3d29e640 100644
--- a/main.nf
+++ b/main.nf
@@ -138,6 +138,7 @@ workflow NFCORE_SEQINSPECTOR {
         samplesheet,
         params.bait_intervals,
         bwamem2,
+        params.checkqc_config,
         fasta,
         params.fastq_screen_references,
         params.multiqc_config,
diff --git a/modules.json b/modules.json
index 25634600..8ef26bfa 100644
--- a/modules.json
+++ b/modules.json
@@ -15,6 +15,11 @@
                         "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a",
                         "installed_by": ["modules"]
                     },
+                    "checkqc": {
+                        "branch": "master",
+                        "git_sha": "389ed64090aa4594276fb3d53923432c7728c5b4",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "1fb5a73bce8e4ac7079b0a9461b23d11e877ad14",
diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml
new file mode 100644
index 00000000..e9be6540
--- /dev/null
+++ b/modules/nf-core/checkqc/environment.yml
@@ -0,0 +1,16 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::sample-sheet=0.13.0
+  - conda-forge::numpy=2.2.4
+  - conda-forge::pandas=2.2.2
+  - conda-forge::pip=25.2
+  - conda-forge::python=3.10.19
+  - conda-forge::tornado=6.3.2
+  - conda-forge::xmltodict=0.13.0
+  - pip:
+      - checkQC==4.1.0
+      - interop==1.4.0
+      - jsonschema==4.26.0
+      - samshee==0.2.12
diff --git a/modules/nf-core/checkqc/main.nf b/modules/nf-core/checkqc/main.nf
new file mode 100644
index 00000000..fc39ee0d
--- /dev/null
+++ b/modules/nf-core/checkqc/main.nf
@@ -0,0 +1,76 @@
+process CHECKQC {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6ec3d6e7260c79ecd92ff53e66337a8f1db4ca8d0a3ba561c35f21fa9acdd6ba/data':
+        'community.wave.seqera.io/library/sample-sheet_numpy_pandas_pip_pruned:0b9dc0869e46a949' }"
+
+    input:
+    tuple val(meta), path(run_dir)
+    path(checkqc_config)
+
+    output:
+    tuple val(meta), path("*checkqc_report.json"), emit: report
+    tuple val("${task.process}"), val('checkqc'), eval('checkqc --version | sed -e "s/checkqc, version //g"'), emit: versions_checkqc, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CheckQC module does not support Conda yet. Please use Docker / Singularity / Podman instead."
+    }
+
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def config = checkqc_config ? "--config $checkqc_config" : ''
+    def input_tar = run_dir.toString().endsWith(".tar.gz") ? true : false
+    def input_dir = input_tar ? run_dir.toString() - '.tar.gz' : run_dir
+
+    """
+    if [ ! -d ${input_dir} ]; then
+        mkdir -p ${input_dir}
+    fi
+
+    if ${input_tar}; then
+        ## Ensures --strip-components only applied when top level of tar contents is a directory
+        ## If just files or multiple directories, place all in ${input_dir}
+
+        if [[ \$(tar -taf ${run_dir} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+            tar \\
+                -C ${input_dir} --strip-components 1 \\
+                -xavf \\
+                ${args2} \\
+                ${run_dir} \\
+                ${args3}
+        else
+            tar \\
+                -C ${input_dir} \\
+                -xavf \\
+                ${args2} \\
+                ${run_dir} \\
+                ${args3}
+        fi
+    fi
+
+    checkqc \
+        $args \
+        $config \
+        --json \
+        $input_dir > checkqc_report.json || true
+
+    # Check if the output JSON file is empty
+    if [[ ! -s checkqc_report.json ]] ; then
+        echo "Error: Empty JSON files. Most likely due to missing files in run directory. See .command.log file for errors."
+        exit 1
+    fi
+    """
+
+    stub:
+    """
+    touch checkqc_report.json
+    """
+}
diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml
new file mode 100644
index 00000000..d979c0d1
--- /dev/null
+++ b/modules/nf-core/checkqc/meta.yml
@@ -0,0 +1,72 @@
+name: "checkqc"
+description: A simple program to parse Illumina NGS data and check it for
+  quality criteria
+keywords:
+  - QC
+  - Illumina
+  - genomics
+tools:
+  - "checkqc":
+      description: "A simple program to parse Illumina NGS data and check it for quality
+        criteria."
+      homepage: "https://github.com/Molmed/checkQC"
+      documentation: "http://checkqc.readthedocs.io/en/latest/"
+      doi: "10.21105/joss.00556"
+      licence:
+        - "GPL v3"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - run_dir:
+        type: file
+        description: |
+          Illumina sequencing run directory
+          Can be directory or a compressed tar (tar.gz) of the directory
+        ontologies: []
+  - checkqc_config:
+      type: file
+      description: CheckQC configuration file
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750
+output:
+  report:
+    - - meta:
+          type: file
+          description: CheckQC report in json format
+          pattern: "*checkqc_report.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464
+      - "*checkqc_report.json":
+          type: file
+          description: CheckQC report in json format
+          pattern: "*checkqc_report.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464
+  versions_checkqc:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - checkqc:
+          type: string
+          description: The name of the tool
+      - 'checkqc --version | sed -e "s/checkqc, version //g"':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - checkqc:
+          type: string
+          description: The name of the tool
+      - 'checkqc --version | sed -e "s/checkqc, version //g"':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matrulda"
diff --git a/nextflow.config b/nextflow.config
index b2708988..fc84962c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,6 +22,9 @@ params {
     igenomes_base                    = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore                  = false
 
+    // CheckQC options
+    checkqc_config                   = null
+
     // Fastqscreen options
     fastq_screen_references          = "${projectDir}/assets/example_fastq_screen_references.csv"
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8d2dfce8..dc82098c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -51,19 +51,20 @@
                 "tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to run",
-                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-sort-amount-asc"
                 },
                 "tools_bundle": {
                     "type": "string",
                     "description": "Select some default setup for the tools to be run, tools can still be used to add tools",
                     "pattern": "^((all|bam|fastq|default|illumina|minimal|ont)?,?)*(?<!,)$",
-                    "fa_icon": "fas fa-window-restore"
+                    "fa_icon": "fas fa-window-restore",
+                    "default": "default"
                 },
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip - overrides any other means of tools selection",
-                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
+                    "pattern": "^((checkqc|fastp|fastqc|fastqe|fastqscreen|fq_lint|kraken2|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats|toulligqc)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-window-close "
                 }
             }
@@ -85,6 +86,12 @@
                     "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.",
                     "fa_icon": "fas fa-window-close "
+                },
+                "checkqc_config": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Path to custom CheckQC config",
+                    "fa_icon": "fas fa-cog"
                 }
             }
         },
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
index 8aca7986..03e7e51b 100644
--- a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -332,6 +332,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
         tools_list << 'picard_collectmultiplemetrics'
         tools_list << 'rundirparser'
         tools_list << 'seqfu_stats'
+        tools_list << 'checkqc'
         tools_list << 'toulligqc'
     }
     if ('bam' in bundle_list) {
@@ -354,6 +355,7 @@ def defineToolsList(input_bundle, input_tools, input_skip) {
     if ('illumina' in bundle_list) {
         tools_list << 'rundirparser'
         tools_list << 'seqfu_stats'
+        tools_list << 'checkqc'
     }
     if ('minimal' in bundle_list) {
         tools_list << 'fastqc'
diff --git a/tests/NovaSeq6000.nf.test b/tests/NovaSeq6000.nf.test
index 79bfd2e7..0531aea5 100644
--- a/tests/NovaSeq6000.nf.test
+++ b/tests/NovaSeq6000.nf.test
@@ -43,7 +43,7 @@ nextflow_pipeline {
                 tools_bundle: null,
                 tools: 'fastqc',
             ]
-        ]
+        ],
     ]
 
     // Generate tests for each scenario
diff --git a/tests/NovaSeq6000.nf.test.snap b/tests/NovaSeq6000.nf.test.snap
index 2faae28a..957fef17 100644
--- a/tests/NovaSeq6000.nf.test.snap
+++ b/tests/NovaSeq6000.nf.test.snap
@@ -994,7 +994,6 @@
                 "Input/output options",
                 "  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/seqinspector/testdata/NovaSeq6000/samplesheet.csv",
                 "  outdir                    : [PATH]/tests/[NFT_HASH]/output",
-                "  tools_bundle              : default",
                 "Reference genome options",
                 "  genome                    : R64-1-1",
                 "  fasta                     : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa",
@@ -1064,7 +1063,7 @@
                 "[NXF_HASH] Submitted process > PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)"
             ]
         ],
-        "timestamp": "2026-03-13T15:53:03.277536715",
+        "timestamp": "2026-03-16T09:53:50.996018165",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -2070,7 +2069,7 @@
         "timestamp": "2026-03-13T15:54:08.436701914",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         }
     },
     "NovaSeq6000 data test relative sample size": {
@@ -3073,7 +3072,7 @@
         "timestamp": "2026-03-13T15:55:15.892319993",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         }
     },
     "NovaSeq6000 data test - No rundirs": {
@@ -4037,7 +4036,7 @@
         "timestamp": "2026-03-13T15:57:07.115797171",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         }
     },
     "NovaSeq6000 data test sample size exceeds available reads": {
@@ -5046,7 +5045,7 @@
         "timestamp": "2026-03-13T15:56:14.759821206",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         }
     },
     "NovaSeq6000 data test - tag collision": {
@@ -5837,7 +5836,7 @@
         "timestamp": "2026-03-13T15:57:49.731500962",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.2"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/tools_checkqc.nf.test b/tests/tools_checkqc.nf.test
new file mode 100644
index 00000000..07a1b024
--- /dev/null
+++ b/tests/tools_checkqc.nf.test
@@ -0,0 +1,31 @@
+def pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+def projectDir = new File('.').absolutePath
+
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+
+    def test_scenario = [
+        [
+            name: "NovaSeq6000 data test - checkqc",
+            params: [
+                tools: 'checkqc',
+                tools_bundle: null
+            ]
+        ],
+        [
+            name: "NovaSeq6000 data test - checkqc with config",
+            params: [
+                checkqc_config: "$projectDir/assets/checkqc_config.yml",
+                tools: 'checkqc',
+                tools_bundle: null
+            ]
+        ]
+    ]
+
+    // Generate tests for each scenario
+    test_scenario.each { scenario ->
+        test(scenario.name, UTILS.getTest(scenario))
+    }
+}
diff --git a/tests/tools_checkqc.nf.test.snap b/tests/tools_checkqc.nf.test.snap
new file mode 100644
index 00000000..85547f6e
--- /dev/null
+++ b/tests/tools_checkqc.nf.test.snap
@@ -0,0 +1,308 @@
+{
+    "NovaSeq6000 data test - checkqc": {
+        "content": [
+            6,
+            {
+                "CHECKQC": {
+                    "checkqc": "4.1.0"
+                }
+            },
+            [
+                "checkqc",
+                "checkqc/checkqc_report.json",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_plots",
+                "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
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+                "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_report.html",
+                "multiqc/group_reports/group2",
+                "multiqc/group_reports/group2/multiqc_data",
+                "multiqc/group_reports/group2/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_plots",
+                "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_report.html",
+                "multiqc/group_reports/lane1",
+                "multiqc/group_reports/lane1/multiqc_data",
+                "multiqc/group_reports/lane1/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_plots",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_report.html",
+                "multiqc/group_reports/test",
+                "multiqc/group_reports/test/multiqc_data",
+                "multiqc/group_reports/test/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/test/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/test/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+            ],
+            [
+                "checkqc_report.json:md5,8245b6a8b8e0e2d247cb7a151d53612f",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18"
+            ],
+            "No BAM files",
+            "No warnings"
+        ],
+        "timestamp": "2026-03-16T09:42:19.096152642",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "NovaSeq6000 data test - checkqc with config": {
+        "content": [
+            6,
+            {
+                "CHECKQC": {
+                    "checkqc": "4.1.0"
+                }
+            },
+            [
+                "checkqc",
+                "checkqc/checkqc_report.json",
+                "multiqc",
+                "multiqc/global_report",
+                "multiqc/global_report/multiqc_data",
+                "multiqc/global_report/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/global_report/multiqc_data/llms-full.txt",
+                "multiqc/global_report/multiqc_data/multiqc.log",
+                "multiqc/global_report/multiqc_data/multiqc.parquet",
+                "multiqc/global_report/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/global_report/multiqc_data/multiqc_citations.txt",
+                "multiqc/global_report/multiqc_data/multiqc_data.json",
+                "multiqc/global_report/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/global_report/multiqc_data/multiqc_sources.txt",
+                "multiqc/global_report/multiqc_plots",
+                "multiqc/global_report/multiqc_plots/pdf",
+                "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/global_report/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/global_report/multiqc_plots/png",
+                "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/global_report/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/global_report/multiqc_plots/svg",
+                "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/global_report/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/global_report/multiqc_report.html",
+                "multiqc/group_reports",
+                "multiqc/group_reports/group1",
+                "multiqc/group_reports/group1/multiqc_data",
+                "multiqc/group_reports/group1/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/group1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group1/multiqc_plots",
+                "multiqc/group_reports/group1/multiqc_plots/pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/group1/multiqc_plots/png",
+                "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/group1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/group1/multiqc_plots/svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/group1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/group1/multiqc_report.html",
+                "multiqc/group_reports/group2",
+                "multiqc/group_reports/group2/multiqc_data",
+                "multiqc/group_reports/group2/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/group2/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.log",
+                "multiqc/group_reports/group2/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/group2/multiqc_plots",
+                "multiqc/group_reports/group2/multiqc_plots/pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/group2/multiqc_plots/png",
+                "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/group2/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/group2/multiqc_plots/svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/group2/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/group2/multiqc_report.html",
+                "multiqc/group_reports/lane1",
+                "multiqc/group_reports/lane1/multiqc_data",
+                "multiqc/group_reports/lane1/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/lane1/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.log",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/lane1/multiqc_plots",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/lane1/multiqc_plots/png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/lane1/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/lane1/multiqc_plots/svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/lane1/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/lane1/multiqc_report.html",
+                "multiqc/group_reports/test",
+                "multiqc/group_reports/test/multiqc_data",
+                "multiqc/group_reports/test/multiqc_data/checkqc_reads-per-sample-plot.txt",
+                "multiqc/group_reports/test/multiqc_data/llms-full.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc.log",
+                "multiqc/group_reports/test/multiqc_data/multiqc.parquet",
+                "multiqc/group_reports/test/multiqc_data/multiqc_checkqc.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_citations.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_data.json",
+                "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt",
+                "multiqc/group_reports/test/multiqc_plots",
+                "multiqc/group_reports/test/multiqc_plots/pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-cnt.pdf",
+                "multiqc/group_reports/test/multiqc_plots/pdf/checkqc_reads-per-sample-plot-pct.pdf",
+                "multiqc/group_reports/test/multiqc_plots/png",
+                "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-cnt.png",
+                "multiqc/group_reports/test/multiqc_plots/png/checkqc_reads-per-sample-plot-pct.png",
+                "multiqc/group_reports/test/multiqc_plots/svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-cnt.svg",
+                "multiqc/group_reports/test/multiqc_plots/svg/checkqc_reads-per-sample-plot-pct.svg",
+                "multiqc/group_reports/test/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
+            ],
+            [
+                "checkqc_report.json:md5,8245b6a8b8e0e2d247cb7a151d53612f",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18",
+                "checkqc_reads-per-sample-plot.txt:md5,32ac72d463abb6df384d43041965b167",
+                "multiqc_checkqc.txt:md5,f2690f77b441c21eeea435c6f8630902",
+                "multiqc_citations.txt:md5,2f5fc28069c07e52fdef3d6d25464b18"
+            ],
+            "No BAM files",
+            "No warnings"
+        ],
+        "timestamp": "2026-03-16T09:52:01.65763035",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/tests/tools_fq_lint.nf.test b/tests/tools_fq_lint.nf.test
index b13a5432..80cd4a40 100644
--- a/tests/tools_fq_lint.nf.test
+++ b/tests/tools_fq_lint.nf.test
@@ -11,6 +11,8 @@ nextflow_pipeline {
             params: [
                 input: pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_wrongpair.csv',
                 continue_with_lint_fail: true,
+                tools: 'fq_lint',
+                tools_bundle: null
             ]
         ],
         [
@@ -18,6 +20,8 @@ nextflow_pipeline {
             params: [
                 input: pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet_wrongpair.csv',
                 continue_with_lint_fail: false,
+                tools: 'fq_lint',
+                tools_bundle: null
             ],
             snapshot_ignore:['Failed','exception'],
             failure:true
@@ -26,6 +30,8 @@ nextflow_pipeline {
             name: "NovaSeq6000 data test - args for fq/lint",
             params: [
                 fq_lint_args: '--disable-validator P001',
+                tools: 'fq_lint',
+                tools_bundle: null
             ]
         ]
     ]
diff --git a/tests/tools_fq_lint.nf.test.snap b/tests/tools_fq_lint.nf.test.snap
index de1fa6d1..50dfbd55 100644
--- a/tests/tools_fq_lint.nf.test.snap
+++ b/tests/tools_fq_lint.nf.test.snap
@@ -1,988 +1,27 @@
 {
     "NovaSeq6000 data test - args for fq/lint": {
         "content": [
-            43,
+            5,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "BWAMEM2_MEM": {
-                    "bwamem2": "2.2.1",
-                    "samtools": "1.22.1"
-                },
-                "FASTQC": {
-                    "fastqc": "0.12.1"
-                },
-                "FASTQSCREEN_FASTQSCREEN": {
-                    "fastqscreen": "0.16.0"
-                },
                 "FQ_LINT": {
                     "fq": "0.12.0"
-                },
-                "PICARD_COLLECTMULTIPLEMETRICS": {
-                    "picard": "3.4.0"
-                },
-                "RUNDIRPARSER": {
-                    "PyYAML": "6.0.2",
-                    "Python": "3.13.2"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.23"
-                },
-                "SAMTOOLS_INDEX": {
-                    "samtools": "1.23"
-                },
-                "SEQFU_STATS": {
-                    "seqfu": "1.22.3"
                 }
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
-                "bwamem2_mem",
-                "bwamem2_mem/Sample1_01.bam",
-                "bwamem2_mem/Sample1_01.bam.bai",
-                "bwamem2_mem/Sample23_03.bam",
-                "bwamem2_mem/Sample23_03.bam.bai",
-                "bwamem2_mem/SampleA_02.bam",
-                "bwamem2_mem/SampleA_02.bam.bai",
-                "bwamem2_mem/Undetermined_05.bam",
-                "bwamem2_mem/Undetermined_05.bam.bai",
-                "bwamem2_mem/sampletest_04.bam",
-                "bwamem2_mem/sampletest_04.bam.bai",
-                "fastqc",
-                "fastqc/Sample1_01_fastqc.html",
-                "fastqc/Sample1_01_fastqc.zip",
-                "fastqc/Sample23_03_fastqc.html",
-                "fastqc/Sample23_03_fastqc.zip",
-                "fastqc/SampleA_02_fastqc.html",
-                "fastqc/SampleA_02_fastqc.zip",
-                "fastqc/Undetermined_05_fastqc.html",
-                "fastqc/Undetermined_05_fastqc.zip",
-                "fastqc/sampletest_04_fastqc.html",
-                "fastqc/sampletest_04_fastqc.zip",
-                "fastqscreen",
-                "fastqscreen/Sample1_01_screen.html",
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-                "picard_base_distribution_by_cycle__Thymine.txt:md5,d0317fe5ef2cf1b692526cb9a18aa50c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,8aafe701b59b4e70ccec86748c7d6eb3",
-                "picard_quality_by_cycle.txt:md5,366ee22c93a11c1335f867020bb03da5",
-                "picard_quality_score_distribution.txt:md5,17d6f490cb59e16a7ed4b04ffaa1a100",
-                "fastq_screen_plot.txt:md5,db7c9231e756a6e5999399a7385e4687",
-                "fastqc-status-check-heatmap.txt:md5,fc37eaf184877ac80b92001a7bf2fa81",
-                "fastqc_overrepresented_sequences_plot.txt:md5,0693849fc324ddf580e2c5a4d910bb4f",
-                "fastqc_per_base_n_content_plot.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,18016152915653e812818194a142e162",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,93f664e18c021aae79ad222fb4cfb393",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,ba96762be2aa842e1d2a606095ffcb7e",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b9044bfe90fd5685137739f52a97ee2c",
-                "fastqc_sequence_counts_plot.txt:md5,42b26ad3758717659763c81852c4f197",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,818f13a5372bad79e54cd984758096c5",
-                "fastqc_sequence_length_distribution_plot.txt:md5,98316a2607a889ae1e7e79a4f64cc740",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,024e1e7f9db3b0906c7aa0904229e176",
-                "multiqc_fastqc.txt:md5,3407d8f06117a65efce4c70f19e91dd1",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,1debd96f9f64c60a8ec742411da51a28",
-                "multiqc_picard_baseContent.txt:md5,afb4046944e302b40faea2233bca535c",
-                "multiqc_picard_quality_by_cycle.txt:md5,6a7552b74dd22410c3cab2c750de792e",
-                "multiqc_picard_quality_score_distribution.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
-                "multiqc_seqfu_mqc.txt:md5,6cdb863a3686fbb772aae5a66925ff23",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,6a7552b74dd22410c3cab2c750de792e",
-                "picard_QualityScoreDistribution_histogram.txt:md5,d6343c5f39942bc3f10c194067e6e9bc",
-                "picard_alignment_readlength_plot.txt:md5,01140e65e813b4ae43aabe662ef2f49a",
-                "picard_alignment_summary.txt:md5,79312cf30761025cc6902811c4165290",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,3c3671ac2aa18d883691d59adbfe3b2b",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6cc2ae1411899de5542321ff1592b192",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,326471bc846a9fb6b54ff38cbdfb8d90",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3132dac406a9b9e1f18af658ab856a5c",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0ed7f750b500e7c5387ea5309e1ef467",
-                "picard_quality_by_cycle.txt:md5,fe4e6ab1c849a4f833eae9a8554ea432",
-                "picard_quality_score_distribution.txt:md5,c0864f8a1269d8ffd7a51abb6bd3ca2e",
-                "fastq_screen_plot.txt:md5,4def6c6a888afe487ab6ebef3ba8a133",
-                "fastqc-status-check-heatmap.txt:md5,61857d2c45cf0c080348047aa34e7525",
-                "fastqc_overrepresented_sequences_plot.txt:md5,7949c64cc6cef77f29349a188fc09656",
-                "fastqc_per_base_n_content_plot.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,0a8bfa32ab04eaaa509dec3c37acb2d2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8c85be0c70129ba739feceddd58f6c75",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,94b975906d8a07e1604e00d4004f7463",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,ec22c8e4836aa726680f0ca767c778a0",
-                "fastqc_sequence_counts_plot.txt:md5,f4341795bdeba588248a74a095a97f8d",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8fc995cb2192a2926eee242681bc3af6",
-                "fastqc_sequence_length_distribution_plot.txt:md5,4513e22583677a4d6167b9094242eb0b",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,fd3074930c72b666f201ae71fa27744b",
-                "multiqc_fastqc.txt:md5,98111f17d1899cad6379e4e56ed11c53",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,3b1929de09267fc1c1a15804cb5bf536",
-                "multiqc_picard_baseContent.txt:md5,ff36be9e2642089aa711c637d3cdba29",
-                "multiqc_picard_quality_by_cycle.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
-                "multiqc_picard_quality_score_distribution.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
-                "multiqc_seqfu_mqc.txt:md5,f821357507fda2d4cfd9299f52fa7dc1",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,9521c83313eaf5f681ac9a75de83a4b7",
-                "picard_QualityScoreDistribution_histogram.txt:md5,90b9e29f22fa16cf2b0c4d92caf2dbb0",
-                "picard_alignment_readlength_plot.txt:md5,9c80659c5c9b2fe9926b789fb67ba6ac",
-                "picard_alignment_summary.txt:md5,27bbb1fcdeecd26641938e5622087c23",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,99c5e961a4d26754e68047c8eb983798",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,44981dd399013d8c06481958be338040",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,b6369a23d3926edb90ae9bfdc6d90526",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,b253d3fca7c07b6a6dfea91725c58102",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,0f2fd628631d42ed5e6a1db22578daaa",
-                "picard_quality_by_cycle.txt:md5,3c34ae2bd2442a816577b1a794add2d6",
-                "picard_quality_score_distribution.txt:md5,0d58c59eac2952e6f71cefc35d4c4477",
-                "fastq_screen_plot.txt:md5,5abb5b9ed2c976f0ad83216ca3186201",
-                "fastqc-status-check-heatmap.txt:md5,323d6082b73ddb6ee33385f5ea4301c1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4e71d8913d40eb06db0f18d74ce6898f",
-                "fastqc_per_base_n_content_plot.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,e6f44d08f4185f680d4748a3b37201e2",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a1dc8a968f32bcf8a9b4c5f43d299dfa",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,e41b6dc1344f1aee379993daff310187",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,76f792b939233b070562cc46617f6371",
-                "fastqc_sequence_counts_plot.txt:md5,36c68522023b8d536c9362403bf03c48",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,9ff0df466790d971b3c7ef838efc0f4f",
-                "fastqc_sequence_length_distribution_plot.txt:md5,9fda632b92e3453f11cd0226484fce8e",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,536c28d7fadc9a76944f93ac9d643272",
-                "multiqc_fastqc.txt:md5,396b4cc0466a6642ec8b954237c42263",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,153c6e6a407ec128b1a02798ca2f1115",
-                "multiqc_picard_baseContent.txt:md5,6349e514552a0b5a0530fa6f311878a5",
-                "multiqc_picard_quality_by_cycle.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
-                "multiqc_picard_quality_score_distribution.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
-                "multiqc_seqfu_mqc.txt:md5,8cced36d66ca9d25d60c006e734aa7e9",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c0c8b4c0197428d4d50e2c532814e1e2",
-                "picard_QualityScoreDistribution_histogram.txt:md5,40e0b6faa75e1b51af42407f7ededb0c",
-                "picard_alignment_readlength_plot.txt:md5,5a19b1f8e2ac49d97f36a7792429419c",
-                "picard_alignment_summary.txt:md5,f9f791b7c569cfae07aef70aa630d40e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,0165f522c84da6b17a286d37dc30abec",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,6fa0d29d40fe7fa24c166b664b6d4f4b",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,bf2426e09ac1ca4773edfc284c220122",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,3cbace572471ccf6c58673181dd0c0ec",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,b317ce09cb7a2be2366b544ea9b20ce6",
-                "picard_quality_by_cycle.txt:md5,7cb705007bc97da8c0da7d93201e6975",
-                "picard_quality_score_distribution.txt:md5,47d684abae0a8f4f09df43e91d54fb9a",
-                "fastq_screen_plot.txt:md5,82ceb9f2109f865d6d1b943441c09550",
-                "fastqc-status-check-heatmap.txt:md5,56b426cd5c030288639533fce7c95ab1",
-                "fastqc_overrepresented_sequences_plot.txt:md5,8e83abdbe7362e64d63339ee31ab3361",
-                "fastqc_per_base_n_content_plot.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,40bc954cc0d58a3197fdf124a40f1ca4",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,e240e30996c81a34b5d1a6b5a98ae254",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,b44d3376d503af12857d494c58b514bb",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,66b5b6d44f398fc9429460c0b9ba3ea9",
-                "fastqc_sequence_counts_plot.txt:md5,6e5804f553f656cffb02f927015d1026",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,fbe41935ea2e2faf7104393b476e5ac5",
-                "fastqc_sequence_length_distribution_plot.txt:md5,e77dc4ab73252c2e09c7452c3b8e8ab3",
-                "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
-                "multiqc_fastq_screen.txt:md5,4fc422d9cb06a1d0248cc578c1eebaa2",
-                "multiqc_fastqc.txt:md5,95c8ffb23baafec625aeb600047515ae",
-                "multiqc_mqc_seq_metadata.txt:md5,5c5f63f044bdcb1ab74a66b896f0b6e7",
-                "multiqc_picard_AlignmentSummaryMetrics.txt:md5,2d05e826f5152fd0143edf7270de1235",
-                "multiqc_picard_baseContent.txt:md5,f3f23899a30a96260d8b5b3020708703",
-                "multiqc_picard_quality_by_cycle.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
-                "multiqc_picard_quality_score_distribution.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
-                "multiqc_seqfu_mqc.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8",
-                "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "picard_MeanQualityByCycle_histogram_1.txt:md5,c7edfc271ab59ecedad0ab046afd3563",
-                "picard_QualityScoreDistribution_histogram.txt:md5,7fa89b52b8bc96dd1074aa07cb5a5a54",
-                "picard_alignment_readlength_plot.txt:md5,c1519319c4942162b05e6225fea10569",
-                "picard_alignment_summary.txt:md5,49f5c0d2cf21a13d5f363cb42cf3790e",
-                "picard_base_distribution_by_cycle__Adenine.txt:md5,466a14fc9c09f9f4de02a00e8763cd2a",
-                "picard_base_distribution_by_cycle__Cytosine.txt:md5,d5854c22df4ac60b8c47c4002d975fe9",
-                "picard_base_distribution_by_cycle__Guanine.txt:md5,c27b5aa2b90397b1302b880dff3ec958",
-                "picard_base_distribution_by_cycle__Thymine.txt:md5,6f2a3e9d03f17a93c69476607a1a580d",
-                "picard_base_distribution_by_cycle__Undetermined.txt:md5,33b70326d8f888ac5a3d99b85f365e43",
-                "picard_quality_by_cycle.txt:md5,0aa028d69d8bb02f0a2bcd0ed08f4235",
-                "picard_quality_score_distribution.txt:md5,a2882ff59902dc95830ed4bdb955561a",
-                "200624_A00834_0183_BHMTFYDRXX_illumina_mqc.yml:md5,29e05fed18bca0e9a857c992b6d59a40",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b",
-                "Sample1_01_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6",
-                "Sample1_01_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a",
-                "Sample23_03_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc",
-                "Sample23_03_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027",
-                "SampleA_02_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775",
-                "SampleA_02_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27",
-                "Undetermined_05_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e",
-                "Undetermined_05_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d",
-                "sampletest_04_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377",
-                "sampletest_04_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2"
-            ],
-            [
-                "Sample1_01.bam:md5,d06ccfde49cc474faebcab2ebf71b324",
-                "Sample23_03.bam:md5,5ff9f554c6255fd07d3841c6616c5031",
-                "SampleA_02.bam:md5,250d0031520e59ee59a7112ab1ea32e1",
-                "Undetermined_05.bam:md5,8fcc158f1e0736b366152d5e187644ca",
-                "sampletest_04.bam:md5,f80371e37421d97499b3bfd55221ed00"
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
+            "No stable content",
+            "No BAM files",
             "No warnings"
         ],
-        "timestamp": "2026-03-12T16:33:49.096054029",
+        "timestamp": "2026-03-16T09:40:34.164513363",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -995,11 +34,9 @@
             ],
             "No stable content",
             "No BAM files",
-            [
-                "WARN: No samples with rundir found, skipping RUNDIRPARSER"
-            ]
+            "No warnings"
         ],
-        "timestamp": "2026-03-13T16:00:47.718722732",
+        "timestamp": "2026-03-16T09:40:03.529857594",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -1007,42 +44,19 @@
     },
     "NovaSeq6000 data test - fq_lint force success": {
         "content": [
-            2,
+            0,
             {
-                "BWAMEM2_INDEX": {
-                    "bwamem2": "2.2.1"
-                },
-                "SAMTOOLS_FAIDX": {
-                    "samtools": "1.23"
-                }
+                
             },
             [
-                "bwamem2_index",
-                "bwamem2_index/bwamem2",
-                "bwamem2_index/bwamem2/genome.fa.0123",
-                "bwamem2_index/bwamem2/genome.fa.amb",
-                "bwamem2_index/bwamem2/genome.fa.ann",
-                "bwamem2_index/bwamem2/genome.fa.bwt.2bit.64",
-                "bwamem2_index/bwamem2/genome.fa.pac",
                 "pipeline_info",
-                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
-                "samtools_faidx",
-                "samtools_faidx/genome.fa.fai"
-            ],
-            [
-                "genome.fa.0123:md5,8af61f4bc59cc2fe7b396db46a2173f3",
-                "genome.fa.amb:md5,657cfdf0628d140d645d8d01a24f0c5f",
-                "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b",
-                "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e",
-                "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc",
-                "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b"
+                "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"
             ],
+            "No stable content",
             "No BAM files",
-            [
-                "WARN: No samples with rundir found, skipping RUNDIRPARSER"
-            ]
+            "No warnings"
         ],
-        "timestamp": "2026-03-12T14:52:51.835298832",
+        "timestamp": "2026-03-16T09:39:43.387936168",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 539201c3..a6f78b08 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -7,6 +7,7 @@
 
 // modules
 include { BWAMEM2_MEM                } from '../modules/nf-core/bwamem2/mem'
+include { CHECKQC                    } from '../modules/nf-core/checkqc'
 include { FASTP                      } from '../modules/nf-core/fastp'
 include { FASTQC                     } from '../modules/nf-core/fastqc'
 include { FASTQE                     } from '../modules/nf-core/fastqe'
@@ -43,6 +44,7 @@ workflow SEQINSPECTOR {
     ch_samplesheet // channel: samplesheet read in from --input
     bait_intervals
     bwamem2_index
+    checkqc_config
     fasta_reference
     fastq_screen_references
     multiqc_config
@@ -115,6 +117,52 @@ workflow SEQINSPECTOR {
         ch_multiqc_files = ch_multiqc_files.mix(RUNDIRPARSER.out.multiqc)
     }
 
+    //
+    // MODULE: CheckQC
+    //
+    if ('checkqc' in tools) {
+
+        // Branch the samplesheet channel based on rundir presence
+        ch_rundir_branch = ch_samplesheet.branch { meta, _reads ->
+            with_rundir: meta.rundir.size() > 0
+            without_rundir: true
+        }
+
+        // Log warnings for samples without rundir
+        ch_rundir_branch.without_rundir.subscribe { meta, _reads ->
+            log.warn("Sample '${meta.id}' does not have a rundir specified")
+        }
+
+        // From samplesheet channel serving (sampleMetaObj, sampleReadsPath) tuples:
+        // --> Create new rundir channel serving (rundirMetaObj, rundirPath) tuples
+        ch_rundir = ch_rundir_branch.with_rundir
+            .map { meta, _reads -> [meta.rundir, meta] }
+            .groupTuple()
+            .map { rundir, metas ->
+                // Collect all unique tags into a list
+                def all_tags = metas.collect { meta -> meta.tags }.flatten().unique()
+                // Create a new meta object whose attributes are...
+                //  1. tags: The list of merged tags, used for grouping MultiQC reports
+                //  2. dirname: The simple name of the rundir, used for setting unique output names in publishDir
+                def dir_meta = [tags: all_tags, dirname: rundir.simpleName]
+                // Return the new structure, to...
+                //  1. Feed into rundir specific processes
+                //  2. Mix with the ch_multiqc_files channel downstream
+                [dir_meta, rundir]
+            }
+
+        ch_rundir.ifEmpty { log.warn("No samples with rundir found, skipping CHECKQC") }
+
+        CHECKQC(
+            ch_rundir,
+            checkqc_config
+                ? file(checkqc_config, checkIfExists: true)
+                : [],
+        )
+
+        ch_multiqc_files = ch_multiqc_files.mix(CHECKQC.out.report)
+    }
+
 
     //
     // MODULE: Run Seqtk sample