mjsull/covid_pipe

COVID pipeline

A simple pipeline for the assembly, consensus calling and annotation of COVID.

This pipeline is somewhat dependent on folder structures and naming schemes used by the HPC/sequencing core at Icahn School of Medicine.

It also has the primer set hard-coded.

Please ensure you understand how it works and what changes will need to be made if you plan on running on your own data. I am happy to help (time permitting) so please reach out.

To run this pipeline first create the conda environment for it to run in.

cd <this directory>

conda env create --file env.yml

conda activate COVID

you may need to update conda before creation

conda update conda

Then for pacbio CCS reads run:

python run_pipeline.py -p <pacbio_ccs_reads.fastq> -o <path/to/output>

Threads can be specified with -t

For Illumina reads run:

python run_pipeline.py -i <sample_folder>

The following folder structure should exist

└───<reads_15kb_primers>'
│   │   <read_prefix>_1.fastq.gz
│   │   <read_prefix>_2.fastq.gz
│
└───<reads_2kb_primers>
    │   <read_prefix>_1.fastq.gz
    │   <read_prefix>_2.fastq.gz

n.b. can be run on one to as many read files as needed, each pair of reads should have it's own folder.

will create pipeline folder in <sample_folder> with output.

running QC

Finally to run QC do python run_QC.py -i <sample_folder> -kb /path/to/kraken_db

on any <sample_folder> that has run successfully.

covid_pipe's Issues

Pipeline not working with long reads option

We try to run the pipeline with the following command:

"""
python run_pipeline.py -p /datagimur/GIMUR2/5_MinION_data/R2-SARS-02C/SARS-CIMBIUR/20201217_2233_MN34569_FAO37349_56f16094/fastq_pass/barcode01/FAO37349_pass_barcode01_df502749_0.fastq -o .
"""

And we get the following error:

"""
Traceback (most recent call last):
File "run_pipeline.py", line 307, in
run_ccs(args)
File "run_pipeline.py", line 214, in run_ccs
% (args.threads, repo_dir, repo_dir, working_dir, args.ccs_reads, working_dir), shell=True).wait()
NameError: name 'working_dir' is not defined

"""

In the function run_css():

"""

def run_ccs(args):
subprocess.Popen("cutadapt -j %s -g file:%s/db/SARS-CoV-2_primers_5prime_anchored.fa -a "
"file:%s/db/SARS-CoV-2_primers_3prime_anchored.fa -o %s/reads.1.fq.gz %s > %s/cutadapt.1.log"
% (args.threads, repo_dir, repo_dir, working_dir, args.ccs_reads, working_dir), shell=True).wait()

"""

We don´t have working_dir variable as not defined in script run_pipeline.py in line 212.

Thanks a lot!!!