Go through and validate test data + list of default steps

CHANGELOG.md

@@ -21,6 +21,9 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#94](https://github.com/nf-core/seqinspector/issues/94) Test data validation
+- [#86](https://github.com/nf-core/seqinspector/issues/86) Update lists of default steps in the pipeline
+- [#84](https://github.com/nf-core/seqinspector/issues/84) Short summary of seqinspector in README.md
 
 ### `Fixed`
 

README.md

@@ -19,7 +19,7 @@
 
 ## Introduction
 
-**nf-core/seqinspector** is a bioinformatics pipeline that ...
+**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencing data to provide comprehensive quality control and exploratory analysis. It performs 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 reports with flexible output options, ranging from individual sample analyses to project-wide summaries, making it particularly useful for sequencing core facilities and research groups with access to sequencing instruments.
 
 <!-- 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
@@ -29,11 +29,12 @@
 
 <!-- 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/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
+4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
+5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 

conf/test.config

@@ -23,8 +23,6 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'seqinspector/testdata/NovaSeq6000/samplesheet.csv'
     fastq_screen_references = "${projectDir}/assets/example_fastq_screen_references.csv"