Introduction

This document describes the output produced by the pipeline.

The directories listed below will be created in the results directory (or species_dir when using a samplesheet) after the pipeline has finished. All paths are relative to the top-level results directory.

The directories comply with Tree of Life's canonical directory structure.

Pipeline overview

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

• Repeat annotation files - Files corresponding to repeat annotation produced by Ensembl
• Pipeline information - Report metrics generated during the workflow execution

All data files are compressed (and indexed) with bgzip.

All Fasta files are indexed with samtools faidx, which allows accessing any region of the assembly in constant time, and samtools dict, which allows identifying a sequence by its MD5 checksum.

All BED files are indexed with tabix in both TBI and CSI modes, unless the sequences are too large.

Repeat annotation files

Here are the files you can expect in the results directory.

└── repeats
    └── ensembl
        ├── GCA_907164925.1.masked.ensembl.bed.gz
        ├── GCA_907164925.1.masked.ensembl.bed.gz.csi
        ├── GCA_907164925.1.masked.ensembl.bed.gz.gzi
        ├── GCA_907164925.1.masked.ensembl.bed.gz.tbi
        ├── GCA_907164925.1.masked.ensembl.fa.dict
        ├── GCA_907164925.1.masked.ensembl.fa.gz
        ├── GCA_907164925.1.masked.ensembl.fa.gz.fai
        ├── GCA_907164925.1.masked.ensembl.fa.gz.gzi
        └── GCA_907164925.1.masked.ensembl.fa.gz.sizes

They all correspond to the repeat-masking analysis run by Ensembl themselves. All files are named after the assembly accession, e.g. GCA_907164925.1.

• GCA_*.masked.ncbi.fasta.gz: Masked assembly in Fasta format
• GCA_*.masked.ncbi.bed.gz: BED file with the coordinates of the regions masked by the Ensembl pipeline

Pipeline information

• pipeline_info/ensemblrepeatdownload/
  • 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.

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.