nf-core/omicsgenetraitassociation
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
Introduction
This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
In the output directory, of a given run of this pipeline, there will be a subdirectory for each sample in the samplesheet where the directory name is the sample name (first field in the samplesheet).
For example, if your samplesheet has two samples, like so:
Then the output directory would have the following structure:
Pipeline overview
The pipeline is built using Nextflow and processes data using the following steps:
- Prepare gene-level trait-association P-values
- Perform (correlated) Meta-Analysis
- Enrichment Analyses
PASCAL
This step aggregates GWAS summary statistics P-values to gene-level scores using PASCAL which accounts for linkage between markers. It provides aggregated gene-level P-values and a manhattan plot for visualization
Output files
pascal/
pascal_out.tsv
: PASCAL gene-level P-valuesmanhattan_plot.png
: manhattan plot
MMAP
This step uses MMAP to perform linear mixed model analysis using gene expression as the main predictor and the trait as the outcome variable. It provides a directory of LMM results for each gene as well as a parsed output as a single csv file.
Output files
mmap/
mmap/
: directory containing single-gene resultsparsed_output_mmap_results.csv
: parsed output file
CMA
This step performs correlated meta-analysis using the CMA package. It provides an output file with the meta P-value and a matrix of tetrachoric correlation coefficients.
Output files
cma/
CMA_meta.csv
: file with meta p-valuetetrachor_sigma.txt
: tetrachoric correlations between input datasets
MEA
This step performs module and gene ontology (GO) enrichment analyses. It provides summaries of each enrichment analysis.
Output files
mea/
master_summary_<sample>.csv
: master summary file with all enrichment analysis results
Pipeline information
Output files
pipeline_info/
- Reports generated by Nextflow:
execution_report.html
,execution_timeline.html
,execution_trace.txt
andpipeline_dag.dot
/pipeline_dag.svg
. - Reports generated by the pipeline:
pipeline_report.html
,pipeline_report.txt
andsoftware_versions.yml
. Thepipeline_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
.
- Reports generated by Nextflow:
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.