Overview

This document describes the output produced when you run nf-core/pixelator.

After a successful run, you should have the following structure in your output folder (e.g. OUTDIR):

work                # Directory containing the nextflow working files
<OUTDIR>            # Finished results in specified location (defined with --outdir)
.nextflow.log       # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.

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

Pipeline stages

The different pipeline stages are described in the introduction section.

pixelator amplicon

Output files

• pixelator
  • amplicon
    • <sample-id>.merged.fastq.gz: Build amplicon reads.
    • <sample-id>.report.json: Pixelator amplicon json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-amplicon.log: Pixelator amplicon log output.

pixelator preqc

Output files

• pixelator
  • preqc
    • <sample-id>.processed.fastq.gz: Processed reads.
    • <sample-id>.failed.fastq.gz: Discarded reads.
    • <sample-id>.report.json: Fastp json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-qc.log: Pixelator preqc and adapterqc log output concatenated.

pixelator adapterqc

Output files

• pixelator
  • adapterqc
    • <sample-id>.processed.fastq.gz: Processed reads.
    • <sample-id>.failed.fastq.gz: Discarded reads.
    • <sample-id>.report.json: Cutadapt json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-qc.log: Pixelator preqc and adapterqc log output concatenated.

pixelator demux

Output files

• pixelator
  • demux
    • <sample-id>.processed-*.fastq.gz: Reads demultiplexed per antibody oligo sequence.
    • <sample-id>.report.json: Demux json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-demux.log: Pixelator demux log output.

pixelator collapse

Output files

• pixelator
  • collapse
    • <sample-id>.collapsed.csv.gz: Edge list matrix.
    • <sample-id>.report.json: Collapse json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-collapse.log: Pixelator collapse log output.

pixelator graph

Output files

• pixelator
  • graph
    • <sample-id>.edgelist.csv.gz: Recovered edgelist after mega-cluster recovery without molecules considered artifacts.
    • <sample-id>.raw_edgelist.csv.gz: Original edgelist with all molecules collapsed.
    • <sample-id>.components_recovered.csv: Original and derived components after mega-cluster recovery.
    • <sample-id>.report.json: Graph json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-cluster.log: Pixelator graph log output.

pixelator annotate

Output files

• pixelator
  • annotate
    • <sample-id>.dataset.pxl: Pixel file with annotations for filtered cells.
    • <sample-id>.raw_components_metrics.csv.gz: Metrics file for all components before cell calling.
    • <sample-id>.report.json: Annotate json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-annotate.log: Pixelator annotate log output.

pixelator analysis

Output files

• pixelator
  • analysis
    • <sample-id>.dataset.pxl: Pixel file with post-analysis results for each cell.
    • <sample-id>.report.json: Analysis json report.
    • <sample-id>.meta.json: Command invocation metadata for downstream reporting.
  • /logs
    • <sample-id>.pixelator-analysis.log: Pixelator analysis log output.

pixelator report

Output files

• pixelator
  • report
    • <sample-id>_report.html: Sample QC report.

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.
  • Metadata file with software versions, environment information and pipeline configuration for debugging: metadata.json