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Pipeline description in README #111

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da0dd18
Test data validated, TODO removed
Patricie34 Mar 26, 2025
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Merge branch 'dev' of https://github.com/nf-core/seqinspector into dev
Patricie34 Mar 26, 2025
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CHANGELOG.md updated
Patricie34 Mar 26, 2025
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List of default steps in README.md
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CHANGELOG.md update
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Pipeline description in README.md
Patricie34 Mar 26, 2025
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Update README.md
Patricie34 Mar 26, 2025
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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`

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7 changes: 4 additions & 3 deletions README.md
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Expand Up @@ -19,7 +19,7 @@

## Introduction

**nf-core/seqinspector** is a bioinformatics pipeline that ...
**nf-core/seqinspector** is a bioinformatics pipeline that that processes raw sequencedata (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.

<!-- 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
Expand All @@ -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/))
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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/))
3. Report read counts and lengths statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
4. Screen reads against references ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
5. Compile QC results into report ([`MultiQC`](http://multiqc.info/))

Hi, Here are some suggestions for updated descriptions that aim to clarify further what each tool does and present them more succinctly. I also changed the MultiQC one as "raw reads" is not accurate when we now have subsampling. Let me know what you think! :)


## Usage

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2 changes: 0 additions & 2 deletions conf/test.config
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Expand Up @@ -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"

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