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Update README.md
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iraiosub authored Dec 19, 2023
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Expand Up @@ -49,21 +49,21 @@ We recommend using Nextflow with `Java 17.0.9` or later.
2. Pull the desired version of the pipeline from the GitHub repository:

```
nextflow pull iraiosub/riboseq-flow -r v1.0.1
nextflow pull iraiosub/riboseq-flow -r v1.0.2
```

3. Run the pipeline on the provided test dataset:

Using Singularity:

```
nextflow run iraiosub/riboseq-flow -r v1.0.1 -profile test,singularity
nextflow run iraiosub/riboseq-flow -r v1.0.2 -profile test,singularity
```

or using Docker:

```
nextflow run iraiosub/riboseq-flow -r v1.0.1 -profile test,docker
nextflow run iraiosub/riboseq-flow -r v1.0.2 -profile test,docker
```

4. Check succesful execution.
Expand All @@ -75,7 +75,7 @@ nextflow run iraiosub/riboseq-flow -r v1.0.1 -profile test,docker
2. Pull the desired version of the pipeline from the GitHub repository:

```
nextflow pull iraiosub/riboseq-flow -r v1.0.1
nextflow pull iraiosub/riboseq-flow -r v1.0.2
```

3. Create a samplesheet `samplesheet.csv` with information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file with 2 columns, and a header row as shown in the example below.
Expand All @@ -92,7 +92,7 @@ sample3,/path/to/file3.fastq.gz
4. Run the pipeline. The typical command for running the pipeline is as follows (the minimum parameters have been specified):

```
nextflow run iraiosub/riboseq-flow -r v1.0.1 \
nextflow run iraiosub/riboseq-flow -r v1.0.2 \
-profile singularity,crick \
-resume \
--input samplesheet.csv \
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