Daytona_combine

A combine of Daytona and Daytona_cl

What to do

The pipeline is a combine of Daytona and Daytona_cl. The SARS-CoV-2 sequences from clearlabs or other sequencing machine, such as illumina, can all be analyzed by the pipeline.

Prerequisites

Nextflow should be installed. The detail of installation can be found in https://github.com/nextflow-io/nextflow.

Python3 is needed.

Singularity is also needed. The detail of installation can be found in https://singularity-tutorial.github.io/01-installation/.

How to run

1) If the sequence datasets are NOT from clearlabs:

1. put your data files into directory /fastqs. Your data file's name should look like "JBS22002292_1.fastq.gz", "JBS22002292_2.fastq.gz". Test data can be found in the directory /fastqs/testdata. If you want to use the test data, copy them to the directory /fastqs.
2. open file "parames.yaml", set the parameters.
3. get into the directory of the pipeline, run "sbatch ./sbatch_flaq_sc2_combine.sh"

2) If the sequence datasets are from clearlabs:

1. put your data files into directories /fastqs, /bams, and /assemblies. Test data can be found in these directories. If you want to use the test data, copy them to the directories /fastqs, /bams, and /assemblies.
2. open file "parames_clearlabs.yaml", set the parameters.
3. get into the directory of the pipeline, run "sbatch ./sbatch_flaq_sc2_combine.sh clearlabs"

Results

All results can be found in the directory /output.