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# Quick Start | ||
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Viralgenie needs two things: | ||
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1. [Nextflow](https://www.nextflow.io/) | ||
2. [Docker](https://www.docker.com/resources/what-container/) - [Singularity](https://docs.sylabs.io/guides/latest/user-guide/introduction.html) - [Conda](https://docs.conda.io/en/latest/) | ||
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```bash | ||
# Install nextflow with conda | ||
conda install nextflow | ||
``` | ||
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Run the pipeline with a small test dataset with docker containers: | ||
```bash | ||
nextflow run Joon-Klaps/viralgenie \ | ||
-profile test,docker | ||
``` | ||
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> For a more complete guide on how to set up Nextflow, Docker, Singularity, and Conda, see the [installation guide](installation.md). | ||
## Running viralgenie with your own samples | ||
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```bash | ||
nextflow run Joon-Klaps/viralgenie \ | ||
-profile test,docker \ | ||
--input my_samplesheet.csv | ||
``` | ||
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An input file contains the paths to the fastq files and the sample names. The input file can be in TSV, CSV, YAML, or JSON format. | ||
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=== "TSV" | ||
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```tsv title="input-samplesheet.tsv" | ||
sample fastq_1 fastq_2 | ||
sample1 AEG588A1_S1_L002_R1_001.fastq.gz AEG588A1_S1_L002_R2_001.fastq.gz | ||
sample2 AEG588A5_S5_L003_R1_001.fastq.gz | ||
sample3 AEG588A3_S3_L002_R1_001.fastq.gz AEG588A3_S3_L002_R2_001.fastq.gz | ||
``` | ||
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=== "CSV" | ||
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```csv title="input-samplesheet.csv" | ||
sample,fastq_1,fastq_2 | ||
sample1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz | ||
sample2,AEG588A5_S5_L003_R1_001.fastq.gz, | ||
sample3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz | ||
``` | ||
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=== "YAML" | ||
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```yaml title="input-samplesheet.yaml" | ||
- sample: sample1 | ||
fastq1: AEG588A1_S1_L002_R1_001.fastq.gz | ||
fastq2: AEG588A1_S1_L002_R2_001.fastq.gz | ||
- sample: sample2 | ||
fastq1: AEG588A5_S5_L003_R1_001.fastq.gz | ||
- sample: sample3 | ||
fastq1: AEG588A3_S3_L002_R1_001.fastq.gz | ||
fastq2: AEG588A3_S3_L002_R2_001.fastq.gz | ||
``` | ||
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=== "JSON" | ||
```json title="samplesheet.json" | ||
[ | ||
{ | ||
"sample": "sample1", | ||
"fastq1": "AEG588A1_S1_L002_R1_001.fastq.gz", | ||
"fastq2": "AEG588A1_S1_L002_R2_001.fastq.gz", | ||
}, | ||
{ | ||
"sample": "sample2", | ||
"fastq1": "AEG588A5_S5_L003_R1_001.fastq.gz", | ||
}, | ||
{ | ||
"sample": "sample3", | ||
"fastq1": "AEG588A3_S3_L002_R1_001.fastq.gz", | ||
"fastq2": "AEG588A3_S3_L002_R2_001.fastq.gz", | ||
} | ||
] | ||
``` | ||
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