EVCpipeline

Workflow Introduction

How to run EVC pipeline

1. Install Nextflow as a conda environment
2. Make sure you have the following folders and files in your working directory:

• main.nf
• nextflow.config
• conf/base.config
• sample.csv
• summary.py

You can find these shared files and folder in /tscc/projects/ps-lalexandrov/shared/EVC_nextflow

3. Prepare your sample.csv file:

patient,status,fastq_1,fastq_2,type,file
RADS10,normal,/path/to/RADS10_normal_1.fastq.gz,/path/to/RADS10_normal_2.fastq.gz,exome,fastq
RADS10,tumor,/path/to/RADS10_tumor_1.fastq.gz,/path/to/RADS10_tumor_2.fastq.gz,exome,fastq

If you are running whole exome files, specify exome for type and genome for whole genome samples in the sample.csv You can use the create_sample_csv.sh to create your sample.csv

4. Due to TSCC memory issue, you may need to modify the temp folder path to some folder in restricted:

• $params.mkdup_temp_dir in the main.nf file (Default: $projectDir/mkdup_tmp)
• $workDir in the nextflow.config file (Default: ./work)

5. Request an interactive node and run Nextflow in your working directory under an interactive node:

# Node requesting
srun -N 1 -n 1 -c 8 --mem 125G -t 24:00:00 -p platinum -q hcp-ddp302 -A ddp302 --pty bash

# Activate your nextflow conda environment
conda activate env_nf

# Export TSCC temp directory to any folder in restricted
export TMPDIR=/some/folder/in/restricted/

# Run nextflow
nextflow run main.nf

# If your pipeline terminates with external error, or the interactive node is killed, you can resume your task after setting up the previous steps again with the following command:
nextflow run main.nf -resume

# Optionally, you can recieve an notifiction email on completion with -N flag:
nextflow run main.nf -N your_email@gmail.com

6. Every process result and report will be stored in the RESULT folder

Tool Versions

Tool	Version
FastQC	v0.12.1
Picard	v2.18.27
samtool	v1.21
bwa-mem2	v2.2.1
Conpair	v0.2
Picard MarkDuplicates	v3.2.0-1
gatk4	v4.6.0.0
mosdepth	v0.3.8
Strelka2	v2.9.10
Mutect2	v4.6.0.0 (gatk)
SAGE	v3.3
MuSE2	v2.1.2