Nextflow RAD-Seq pipeline

Overview

This is a RAD-Seq pipeline that generally follows

Data -> FastQC -> Trimmomatic -> FastQC -> process_radtags
-> ustacks -> cstacks -> sstacks -> tsv2bam -> gstacks
-> populations -> multiqc

Running

1. Clone the repository

2. Place your raw data into data/fastq. The data can be raw fastq, or gzip compressed fastq (recommended).

3. Edit data/metadata.csv. 3.1 Do not change the header row, it is used internally 3.2 File paths should be either absolute or relative to the project root (this git repo)

4. Adapt nextflow.config if necessary

5. Start the pipeline: nextflow run main.nf

6. Generate template for materials and methods: nextflow run materials.nf

Example metadata.csv

• RF: (string) Path to first PE read
• RS: (string) Path to second PE read
• Id: (string) A sample name. Avoid spaces and special characters. This should be unique
• NumId: (integer) A numeric sample id. This should be unique
• Population: (string) the population this sample belongs to. If a sample belongs to multiple populations, enter all delimited by a |, e.g. PopA|PopB|PopC

RF,RS,Id,NumId,Population
./data/fastq/my_first_sample_1.fq.gz,./data/fastq/my_first_sample_2.fq.gz,first,1,default
./data/fastq/my_second_sample_1.fq.gz,./data/fastq/my_second_sample_2.fq.gz,second,2,default