nf-core · maxulysse · Nov 7, 2025 · Nov 7, 2025 · Nov 7, 2025 · Nov 7, 2025
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -82,6 +82,12 @@ If you wish to contribute a new step, please use the following coding standards:
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
+### Things to consider regarding displaying results for a new tool
+
+- If a MultiQC module exist for the tool, use the standard settings for it to start with.
+- If no Multiqc module exists, the results of the tool should be made available in the results directory.
+- If a tool doesn’t produce output files, the stdout should be channeled into a output file that can be accessible from the outdir of the pipeline.
+
 ### Default values
 
 Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -24,9 +24,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test
+.nf-test.log
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,11 +1,16 @@
 lint:
+  multiqc_config: false
   files_exist:
     - tests/default.nf.test
   files_unchanged:
     - .github/CONTRIBUTING.md
+    - docs/images/nf-core-seqinspector_logo_dark.png
+    - docs/images/nf-core-seqinspector_logo_light.png
+    - assets/nf-core-seqinspector_logo_light.png
   nextflow_config:
     - config_defaults:
         - params.fastq_screen_references
+  nf_test_content: false
 nf_core_version: 3.5.1
 repository_type: pipeline
 template:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,8 +9,64 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#2](https://github.com/nf-core/seqinspector/pull/2) Input workflow and schema definition
+- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane
+- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
+- [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI
+- [#53](https://github.com/nf-core/seqinspector/pull/53), [#64](https://github.com/nf-core/seqinspector/pull/64) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI
+- [#56](https://github.com/nf-core/seqinspector/pull/56) Added SeqFu stats module
+- [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
+- [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
+- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
+- [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
+- [#100](https://github.com/nf-core/seqinspector/pull/100) Added official logos
+- [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#106](https://github.com/nf-core/seqinspector/pull/106) Parse rundir metadata
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Update lists of default steps in the pipeline (#86)
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Test data validation (#94)
+- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns
+- [#111](https://github.com/nf-core/seqinspector/pull/111) Short summary of seqinspector in README.md (#84)
+- [#127](https://github.com/nf-core/seqinspector/pull/127) Added alignment tools - bwamem2 - index and mem
+- [#128](https://github.com/nf-core/seqinspector/pull/128) Added Picard tools - Collect Multiple Mterics to collect QC metrics
+- [#132](https://github.com/nf-core/seqinspector/pull/132) Added a bwamem2 index params for faster output
+- [#135](https://github.com/nf-core/seqinspector/pull/135) Added index section to MultiQC reports to facilitate report navigation (#125)
+- [#148](https://github.com/nf-core/seqinspector/pull/148) Add Tubemap
+- [#151](https://github.com/nf-core/seqinspector/pull/151) Added a prepare_genome subworkflow to handle bwamem2 indexing
+- [#156](https://github.com/nf-core/seqinspector/pull/156) Added relative sample_size and warning when a sample has less reads than desired sample_size
+- [#159](https://github.com/nf-core/seqinspector/pull/159) Added a subworkflow QC_BAM including picard_collecthsmetrics for alignment QC of hybrid-selection data
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
+
 ### `Fixed`
 
+- [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided
+- [#77](https://github.com/nf-core/seqinspector/pull/77) Use a params for fastqscreen csv file, and not the hardcoded example one
+- [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
+- [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
+- [#108](https://github.com/nf-core/seqinspector/pull/108) Go through and validate test data (#94)
+- [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
+- [#121](https://github.com/nf-core/seqinspector/pull/121) Cleanup sample naming for MultiQC report (#105)
+- [#150](https://github.com/nf-core/seqinspector/pull/150) Fix pipeline linting issues
+- [#162](https://github.com/nf-core/seqinspector/pull/162) Fix bugs in qc_bam and prepare_genome subworkflows and add tests
+- [#163](https://github.com/nf-core/seqinspector/pull/163) Run fastqscreen with subsampled data if available
+
+### `Changed`
+
+- [#15](https://github.com/nf-core/seqinspector/pull/15) Template update for nf-core/tools v2.14.1
+- [#26](https://github.com/nf-core/seqinspector/pull/26), [#49](https://github.com/nf-core/seqinspector/pull/49) Template update for nf-core/tools v3.0.2
+- [#69](https://github.com/nf-core/seqinspector/pull/69) Template update for nf-core/tools v3.1.0
+- [#72](https://github.com/nf-core/seqinspector/pull/72) Template update for nf-core/tools v3.1.2dev0
+- [#74](https://github.com/nf-core/seqinspector/pull/74) Template update for nf-core/tools v3.2.0
+- [#114](https://github.com/nf-core/seqinspector/pull/114) Update CI
+- [#133](https://github.com/nf-core/seqinspector/pull/133) Template update for nf-core/tools v3.4.1
+- [#144](https://github.com/nf-core/seqinspector/pull/144) Template update for nf-core/tools v3.5.1
+- [#145](https://github.com/nf-core/seqinspector/pull/145) Remove outdated comments
+- [#148](https://github.com/nf-core/seqinspector/pull/148), [#152](https://github.com/nf-core/seqinspector/pull/152), [#153](https://github.com/nf-core/seqinspector/pull/153) Update documentation
+- [#158](https://github.com/nf-core/seqinspector/pull/158) Moved picard_collectmultiplemetrics to the subworkflow QC_BAM
+- [#164](https://github.com/nf-core/seqinspector/pull/164) Refactor local subworkflow and pipeline tests
+
 ### `Dependencies`
 
+- [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
+
 ### `Deprecated`
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -14,10 +14,32 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [SeqFu](https://telatin.github.io/seqfu2/)
+
+> Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. doi.org/10.3390/bioengineering8050059
+
+- [FastQ Screen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
+
+> Wingett SW and Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control [version 2; referees: 4 approved]. F1000Research 2018, 7:1338 (https://doi.org/10.12688/f1000research.15931.2)
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [Seqtk](https://github.com/lh3/seqtk)
+
+- [BWAMEM2](https://ieeexplore.ieee.org/abstract/document/8820962)
+
+> 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
+
+- [SAMTOOLS](https://academic.oup.com/bioinformatics/article/25/16/2078/204688)
+
+> Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
+
+- [Picard Tools](https://broadinstitute.github.io/picard/)
+
+> Broad Institute, “Picard Toolkit.” 2019. GitHub Repository. https://broadinstitute.github.io/picard/
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

diff --git a/README.md b/README.md
@@ -21,43 +21,58 @@
 
 ## Introduction
 
-**nf-core/seqinspector** is a bioinformatics pipeline that ...
-
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
-
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/nf-core-seqinspector_logo_light.png">
+  <img alt="Fallback image description" src="docs/images/nf-core-seqinspector_logo_light.png">
+</picture>
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-seqinspector-logo-hex-dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/nfcore-seqinspector-logo-hex-light.png">
+  <img alt="Fallback image description" src="docs/images/nfcore-seqinspector-logo-hex-light.png">
+</picture>
+
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequence data (FASTQ) to provide comprehensive quality control. It can perform subsampling, quality assessment, duplication level analysis, and complexity evaluation on a per-sample basis, while also detecting adapter content, technical artifacts, and common biological contaminants. The pipeline generates detailed MultiQC reports with flexible output options, ranging from individual sample reports to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments. If provided, nf-core/seqinspector can also parse statistics from an Illumina run folder directory into the final MultiQC reports.
+
+<!-- TODO: add a search tool that accepts a tree for `Compatibility with Data`. -->
+
+| Tool Type           | Tool Name                                                                                                           | Tool Description                                                                              | Compatibility with Data | Dependencies                                                                                                              | Default tool |
+| ------------------- | ------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------ |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` 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`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | 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          |
+| `QC`                | [`SeqFu Stats`](https://github.com/telatin/seqfu2)                                                                  | Sequence statistics                                                                           | [RNA, DNA]              | [N/A]                                                                                                                     | yes          |
+| `QC`                | [`Picard collect multiple metrics`](https://broadinstitute.github.io/picard/picard-metric-definitions.html)         | Collect multiple QC metrics                                                                   | [RNA, DNA]              | [Bwamem2, SAMtools, `--genome`]                                                                                           | yes          |
+| `QC`                | [`Picard_collecthsmetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard) | Collect alignment QC metrics of hybrid-selection data.                                        | [RNA, DNA]              | [Bwamem2, SAMtools, `--fasta`, `--run_picard_collecths_metrics`, `--bait_intervals`, `--target_intervals` (`--ref_dict`)] | no           |
+| `Reporting`         | [`MultiQC`](http://multiqc.info/)                                                                                   | Present QC for raw reads                                                                      | [RNA, DNA, synthetic]   | [N/A]                                                                                                                     | yes          |
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/seqinspector_tubemap_V1.0_dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/seqinspector_tubemap_V1.0.png">
+  <img alt="Fallback image description" src="docs/images/seqinspector_tubemap_V1.0.png">
+</picture>
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,fastq_1,fastq_2,rundir,tags
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/seqinspector \
    -profile <docker/singularity/.../institute> \
@@ -78,11 +93,11 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/seqinspector was originally written by Adrien Coulier.
+nf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/) and [Clinical Genomics Stockholm](https://clinical.scilifelab.se/).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [@mahesh-panchal](https://github.com/mahesh-panchal)
 
 ## Contributions and Support
 
@@ -92,9 +107,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/seqinspector for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

diff --git a/assets/example_fastq_screen_references.csv b/assets/example_fastq_screen_references.csv
@@ -0,0 +1,4 @@
+name,dir,basename,aligner
+Ecoli,s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/,genome,bowtie2
+PhiX,s3://ngi-igenomes/igenomes/PhiX/Illumina/RTA/Sequence/Bowtie2Index/,genome,bowtie2
+Scerevisiae,s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/NCBI/build3.1/Sequence/Bowtie2Index/,genome,bowtie2