output.md

assessPool: Output

Introduction

This document describes the output produced by the pipeline.

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.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• Pipeline information - Report metrics generated during the workflow execution

Index

Output files

• index/
  • *.fai/gzi: FAI index of FASTA reference genome/assembly.
  • *.tbi: VCF index.

Results from calling samtools faidx on the reference assembly and tabix on the input VCF.

Filtering results

Output files

• filter/
  • incremental/
    • VCF files (*.vcf.gz) and their associated index files (*.tbi) containing results of stepwise filtering operations.
  • bcftools/
    • Results of cumulative filtering operations performed using bcftools (*.vcf.gz, *.tbi)
  • vcftools/
    • Results of cumulative filtering operations performed using cftools (*.vcf.gz, *.tbi)

Results of VCF filtering. Contains both stepwise and and cumulative filter operations.

grenedalf sync

Output files

• sync/
  • pairwise/
    • <project>_<pool1>-<pool2>.sync: Individual (headerless) pairwise sync file.
  • <project>_sync.sync: Sync file (in grenedalf headered format) for all pools.

Sync files generated from input VCF (or copied / filtered from input sync file).

Fisher's test results

Output files

• fisher/
  • assesspool/*.tsv: pairwise Fisher's test results using built-in assessPool method
  • popoolation/*.fisher: pairwise Fisher's test results using PoPoolation2
  • combined/<project>.fisher: All concatenated pairwise Fisher's test results

Results of Fisher's exact test calculations for each selected calculation method, both concatenated and single pairwise comparisons.

F_st results

Output files

• fst/
  • grenedalf/*.tsv: F_st results calculated using grenedalf.
  • popoolation/*.fst: F_st results calculated using PoPoolation2.
  • poolfstat/*.tsv: F_st results calculated using poolfstat.
  • <project>.fst: Concatenated pairwise F_st results for all methods

Pairwise F_st results by individual calculation method and concatenated.

Pipeline information

Output files

• 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.