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adamrtalbot merged 3 commits into from
Mar 26, 2025
Merged

Update README.md #1518

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befff41
Update README.md
AlenaNik Mar 19, 2025
776196f
Update CHANGELOG.md
AlenaNik Mar 25, 2025
36d7abd
Merge branch 'dev' into master
AlenaNik Mar 25, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -44,6 +44,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1474](https://github.com/nf-core/rnaseq/pull/1474) - Bump versions to 3.18.0
- [PR #1475](https://github.com/nf-core/rnaseq/pull/1475) - Fix log publishing around umitools/ umicollapse
- [PR #1447](https://github.com/nf-core/rnaseq/pull/1447) - Add tutorial series for analysing count data
- [PR #1518](https://github.com/nf-core/rnaseq/pull/1518) - Remove duplicated text in README.md

## Parameters

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9 changes: 2 additions & 7 deletions README.md
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Expand Up @@ -74,10 +74,8 @@ CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,a

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and will be automatically inferred if set to `auto`.

> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).

Now, you can run the pipeline using:

Expand All @@ -90,9 +88,6 @@ nextflow run nf-core/rnaseq \
-profile <docker/singularity/.../institute>
```

> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).

For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).

## Pipeline output
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