Introduction Usage Output Results

Introduction

This document describes the output produced by the nf-core/seqsubmit pipeline.

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

Pipeline overview

The pipeline is built using Nextflow and performs automated submission of sequence data to ENA. Exact steps and generated outputs depend on the data type and --mode executed (mags, bins or metagenomic_assemblies).

mags and bins outputs

When --mode mags or --mode bins is used, results are written under mags/ or bins/.

Output files
  • <mode>/
    • genomes_metadata.csv: tabular metadata assembled for submission.
    • upload/manifests/: manifests generated by genome_uploader.
    • databases/checkm2/: downloaded CheckM2 database file (when downloaded during the run).
    • databases/cat_pack/: prepared CAT_pack database directories (when generated during the run).
    • <sample>/coverage/: coverm genome output for samples where genome_coverage had to be computed.
    • <sample>/rna/barrnap/: barrnap output GFF for samples where RNA_presence had to be inferred.
    • <sample>/rna/trnascanse/: tRNAscan-SE outputs for the same RNA inference step.
    • <sample>/taxonomy/: CAT/BAT taxonomic classification for samples where NCBI_lineage was missing.
    • <sample>/checkm2/: CheckM2 reports for samples where completeness/contamination metadata had to be computed.
    • <sample>/upload/webin_cli/: Webin-CLI wrapper output TSV with accessions for submitted genomes.

Many of these per-sample directories are conditional. For example, if genome_coverage is already provided in the samplesheet, the corresponding coverage/ directory will not be created for that sample.

metagenomic_assemblies outputs

When --mode metagenomic_assemblies is used, results are written under metagenomic_assemblies/.

Output files
  • metagenomic_assemblies/
    • <sample>_assembly_metadata.csv: per-assembly metadata CSV generated for manifest creation.
    • <sample>/coverage/: coverm contig output for samples where coverage had to be calculated from reads.

Assembly study registration, manifest generation, and Webin-CLI submission are executed by the workflow, but their intermediate outputs are not currently published into --outdir by the pipeline.

Common outputs

MultiQC

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.

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
  • 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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