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Prepare the index.csv file. This file will contain a list of sample ids and the full path to the paired samples. Read 1 and Read 2 must be specified separately.
EG:
| Code Block | ||
|---|---|---|
| ||
sampleid,read1,read2 sample01,/full/path/to/sample01_r1.fq.gz,/full/path/to/sample01_r2.fq.gz |
Step 3:
Create a nextflow.config file (if needed). If you need to override any of the pipeline defaults, put them in this file.
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