nanoporeReads_dataTransfer

A pipeline to transfer the Nanopore reads to the end users

Usage

mamba env create -f env.yml
mamba activate ontPipe;
python ont_pipeline.py

Example input path:

../path/to/flowcell/
├── drift_correction_FAL82553_acfbfd23.csv
├── duty_time_FAL82553_acfbfd23.csv
├── fast5
├── final_summary_FAL82553_acfbfd23.txt
├── mux_scan_data_FAL82553_acfbfd23.csv
├── report_FAL82553_20200319_1033_c25a4aea.md
├── Samplesheet.csv
├── sequencing_summary_FAL82553_acfbfd23.txt
└── throughput_FAL82553_acfbfd23.csv

Example output path for bioinfo. core:

../output_path/to/flowcell/
├── drift_correction_FAL82553_acfbfd23.csv
├── duty_time_FAL82553_acfbfd23.csv
├── fast5
├── final_summary_FAL82553_acfbfd23.txt
├── mux_scan_data_FAL82553_acfbfd23.csv
├── report_FAL82553_20200319_1033_c25a4aea.md
├── Samplesheet.csv
├── sequencing_summary_FAL82553_acfbfd23.txt
├── throughput_FAL82553_acfbfd23.csv
├── FASTQC_Project_number_User_PI
└── Project_number_User_PI
    └── Sample_its_name
        └── Sample_name.fastq.gz

Example output path for a user:

../user_path/to/flowcell/
├── FASTQC_Project_number_User_PI
├── Project_number_User_PI
|   └── Sample_its_name
|       └── Sample_name.fastq.gz
└── Analysis_number_User_PI
    └── mapping_on_organism
        ├── organism_genome.fa
        ├── organism_genome.mmi
        ├── sample.bam
        └── sample.bam.bai