Introduction Usage Output Results

Introduction

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory:

results/
├── fastqc/              # Individual HTML reports for specified fastq files, raw sequencing QC
├── fitness/             # Merged variant count tables, fitness and error estimates, replicate correlations and heatmaps
├── intermediate_files/  # Raw alignments, raw and pre-filtered variant count tables, QC reports
├── library_QC/          # Sample-specific PDF visualizations: position-wise sequencing coverage, count heatmaps, etc.
├── multiqc/             # Shared HTML reports for all fastq files, raw sequencing QC
├── pipelineinfo/        # Nextflow helper files for timeline and summary report generation
├── timeline.html        # Nextflow timeline for all tasks
└── report.html          # Nextflow summary report incl. detailed CPU and memory usage per for all tasks

FastQC

FastQC gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the FastQC help pages.

Output files
  • fastqc/
    • *_fastqc.html: FastQC report containing quality metrics.
    • *_fastqc.zip: Zip archive containing the FastQC report, tab-delimited data file and plot images.

MultiQC

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.### Pipeline information

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

Intermediate files

This directory is created during the first series of steps of the pipeline, featuring raw read alignments, filtering and variant counting.

Output files
  • intermediate_files/
    • aa_seq.txt:
    • bam_files/bwa:
    • bam_files/filtered:
    • bam_files/premerged:
    • gatk:
    • possible_mutations.csv:
    • processed_gatk_files:

Library QC

This directory is created during the second series of steps of the pipeline, featuring various QC visualisations for each sample.

Output files
  • library_QC/
    • counts_heatmap.pdf:
    • counts_per_cov_heatmap.pdf:
    • logdiff_plot.pdf:
    • logdiff_varying_bases.pdf:
    • rolling_counts_per_cov.pdf:
    • rolling_counts.pdf:
    • rolling_coverage.pdf:
    • SeqDepth.pdf (optional):

Fitness

This directory is created during the final series of steps of the pipeline, featuring fitness and fitness error estimates (when DMS input/output sample groups are specified).

Output files
  • fitness/
    • counts_merged.tsv: summarised gene variant counts across all input and output samples.
    • default_results/fitness_estimation_count_correlation.pdf:
    • default_results/fitness_estimation_fitness_correlation.pdf:
    • default_results/fitness_heatmap.pdf:
    • default_results/fitness_estimation.tsv:
    • DiMSum_results/dimsum_results (optional):

Pipeline Info

  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter’s are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
    • Parameters used by the pipeline run: params.json.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
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