RNAseq Nextflow Pipeline

Step 1: Clone pipeline into your project directory that contains the fastq files.

git clone https://github.com/Apompetti-Cori/RNAseq_Nextflow.git .

You will now have a folder in your directory called RNAseq_Nextflow.

Step 2: Create csv file explaining the samples

• Use sample_table_template.csv as a guide for your sample table.
• First column should be sample containing sample ID's
• Consequent columns should be r1_L1, r1_L2, r1_L3, r1_L4, r2_L1, r2_L2, r2_L3, r2_L4
  • Example: a single end fastq should have a sample ID and a file name inhabiting the r1_L1 column
    • If it is multilane, it should have the other lanes inhabiting the other r1_L* columns
  • Example: a paired end fastq should have a sample ID and file names inhabiting the r1_L1 and r2_L1 columns
    • If it is multilane, it should have the other lanes inhabiting the other r1_L* columns and r2_L* columns
  • Essentially, multilane files will be concatenated together into their respective reads and fed into the pipleine accordingly