Pipeline Outputs

Top-level reports

If the pipeline was ran with params.collate = "yes" then at the top-level there will be a CSV file containing the reports collated using TB-Profiler/tbtAMR (depending on the choice made with params.resistance_profiler = "<profiler>"; as well as one for NTM-profiler. Both are contingent of Lodestone identifying samples as Mycobacterium tuberculosis or Non-tuberculous mycobacteria, respectively.

The first workflow in the pipeline (getVersions.nf) will also generate a versions.json file which will collect versions listed in the Singularity definition files. This will only be meaningful if the pipeline is ran in a container.

Sample-level reports

 <sample_name>/
    ├── <sample_name>_afanc_report.json
    ├── <sample_name>_kraken_report.json
    ├── <sample_name>_report.json
    ├────── output_bam/
    │            ├── <sample_name>.bam
    │            ├── <sample_name>.bam.bai
    │            ├── <sample_name>_alignmentStats.json     
    ├────── output_reads/
    ├────── output_vcfs/
    ├────── raw_read_QC_reports/  
    ├────── speciation_reports_for_reads_postFastP/