From da0dd184f2094fdfdb29b5c7f219c0300949e88e Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 10:50:35 +0100
Subject: [PATCH 1/5] Test data validated, TODO removed

---
 conf/test.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 0ebc405..1b222be 100644
--- a/conf/test.config
+++ b/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"
 

From 336dc44c053a0aede20ce4db7b453ceaf1031b43 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 11:02:45 +0100
Subject: [PATCH 2/5] CHANGELOG.md updated

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0062af4..b06aa3c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ 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
 
 ### `Fixed`
 

From cb9e70f13fc794350d9b42101cbd3a6a13f57d1c Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 12:29:06 +0100
Subject: [PATCH 3/5] List of default steps in README.md

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6cf36dc..3582178 100644
--- a/README.md
+++ b/README.md
@@ -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
 

From c07cf1c12eb9b7f47ba02bd633aaf17391749ee7 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 12:30:32 +0100
Subject: [PATCH 4/5] CHANGELOG.md update

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b06aa3c..6562709 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#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
 
 ### `Fixed`
 

From 1824be0bafaf07a43bb6a4117f3fda2661343915 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 26 Mar 2025 13:54:02 +0100
Subject: [PATCH 5/5] Pipeline description in README.md

---
 CHANGELOG.md | 1 +
 README.md    | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6562709..eb520ff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#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`
 
diff --git a/README.md b/README.md
index 3582178..29e031d 100644
--- a/README.md
+++ b/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