A combine of Daytona and Daytona_cl
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.
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/.
- 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.
- open file "parames.yaml", set the parameters.
- get into the directory of the pipeline, run "sbatch ./sbatch_flaq_sc2_combine.sh"
- 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.
- open file "parames_clearlabs.yaml", set the parameters.
- get into the directory of the pipeline, run "sbatch ./sbatch_flaq_sc2_combine.sh clearlabs"
All results can be found in the directory /output.