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chbk committed Jun 21, 2021
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Expand Up @@ -11,7 +11,7 @@ To use this pipeline, simply clone or download this repository, and install the

Try out this nextflow pipeline with:

./nextflow-run FAANG/analysis-TAGADA --revision 1.0.1 --output directory --profile test docker
./nextflow-run FAANG/analysis-TAGADA --revision 1.0.2 --output directory --profile test docker

The `./nextflow-run` launcher script replaces the `nextflow run` command and grants these benefits:
- Options can receive multiple space-separated parameters and unquoted globs.
Expand Down Expand Up @@ -90,7 +90,7 @@ The pipeline executes the following main processes:
The annotations of long non-coding RNAs are saved to `output/annotation`.
9. __Quantify__ genes and transcripts with [StringTie](https://github.com/gpertea/stringtie), and __format__ them into tabulated files.
The TPM values and read counts for each annotation are saved to `output/quantification`.
10. Aggregates quality controls into a __report__ with [MultiQC](https://github.com/ewels/MultiQC).
10. Aggregate quality controls into a __report__ with [MultiQC](https://github.com/ewels/MultiQC).
The report is saved to `output/control`.


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