nf-core · maxulysse · Mar 12, 2026 · Mar 11, 2026 · Mar 11, 2026 · Mar 11, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#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
 - [#206](https://github.com/nf-core/seqinspector/pull/206) Added FASTQE for more comprehensive QC of FASTQ files
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -18,6 +18,10 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [Fastp](https://doi.org/10.1093/bioinformatics/bty560)
+
+  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, September 2018, Pages i884–i890.
+
 - [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)

diff --git a/README.md b/README.md
@@ -32,7 +32,8 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 
 | 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           |
+| `Subsampling`       | [`Seqtk`](https://github.com/lh3/seqtk)                                                                             | Global subsampling of reads. Only performs subsampling if `--sample_size` parameter is given. | [RNA, DNA]              | [N/A]                                                                                   | no           |
+| `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`                | [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)                                              | Read QC                                                                                       | [RNA, DNA]              | [N/A]                                                                                   | yes          |
@@ -56,6 +57,7 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
 | Tool        | Version |
 | ----------- | ------- |
 | bwamem2     | 2.3     |
+| fastp       | 1.1.0   |
 | fastqc      | 0.12.1  |
 | fastqe      | 0.5.2   |
 | fastqscreen | 0.16.0  |

diff --git a/conf/modules.config b/conf/modules.config
@@ -22,6 +22,7 @@ process {
 
     withName: FASTQC {
         ext.args = '--quiet'
+        ext.prefix = { "${meta.id}" }
     }
 
     withName: SEQFU_STATS {

diff --git a/docs/output.md b/docs/output.md
@@ -48,6 +48,22 @@ 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/).
 
+### FastP
+
+[FastP](https://github.com/OpenGene/fastp) is a tool designed to provide all-in-one preprocessing for FastQ files and as such is used for trimming and splitting.
+The resulting trimmed files are not published.
+We only keep the reports for MultiQC and the pipeline report.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `fastp/`
+  - `*.fastp.html`: FastP HTML report.
+  - `*.fastp.json`: FastP report containing quality metrics in JSON format.
+  - `*.fastp.log`: FastP log file containing quality metrics.
+
+</details>
+
 ### FASTQE
 
 <details markdown="1">

diff --git a/modules.json b/modules.json
@@ -15,6 +15,11 @@
                         "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a",
                         "installed_by": ["modules"]
                     },
+                    "fastp": {
+                        "branch": "master",
+                        "git_sha": "1fb5a73bce8e4ac7079b0a9461b23d11e877ad14",
+                        "installed_by": ["modules"]
+                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",

diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -51,7 +51,7 @@
                 "tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to run",
-                    "pattern": "^((fastqc|fastqe|fastqscreen|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
+                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-sort-amount-asc"
                 },
                 "tools_bundle": {
@@ -63,7 +63,7 @@
                 "skip_tools": {
                     "type": "string",
                     "description": "Comma-separated string of tools to skip - overrides any other means of tools selection",
-                    "pattern": "^((fastqc|fastqe|fastqscreen|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
+                    "pattern": "^((fastp|fastqc|fastqe|fastqscreen|picard_collecthsmetrics|picard_collectmultiplemetrics|rundirparser|seqfu_stats)?,?)*(?<!,)$",
                     "fa_icon": "fas fa-window-close "
                 },
                 "sort_bam": {