element_cleanup is a simple Nextflow pipeline designed to clean up sequencing data generated on the Aviti Element platform. The pipeline comes pre-configured with known Aviti-specific contaminants that commonly arise from the protocols used.

While a default contaminant FASTA is included, it is highly recommended to either review this file or provide a custom contaminant FASTA tailored to your specific experimental setup.

element_cleanup is supplied with a configuration file optimized for the SciNet Ceres cluster. Any nf-core configuration should be a direct substitution.

The input sample sheet should be a CSV file with the following format:

sample,r1,r2
Sample_01,/full/path/to/Sample_01_R1.fastq.gz,/full/path/to/Sample_01_R2.fastq.gz
Sample_02,/full/path/to/Sample_02_R1.fastq.gz,/full/path/to/Sample_02_R2.fastq.gz

To run the pipeline on Ceres:

nextflow run element_cleanup/ -c element_cleanup/configs/ceres/ceres.cfg \
    --project_name Project_Name \
    --sample_sheet /full/path/to/samplesheet.csv \
    --workflow_opt cleanup_pe

nextflow run element_cleanup/ -c element_cleanup/configs/ceres/ceres.cfg \
    --project_name Project_Name \
    --sample_sheet /full/path/to/samplesheet.csv \
    --workflow_opt cleanup_se

nextflow run element_cleanup/ -c element_cleanup/configs/ceres/ceres.cfg \
    --project_name Project_Name \
    --sample_sheet /full/path/to/samplesheet.csv \
    --workflow_opt multiqc