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
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
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
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
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
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
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
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
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
pixelator
report
<sample-id>_report.html
: Sample QC report.
Pipeline information
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
. - Metadata file with software versions, environment information and pipeline configuration for debugging:
metadata.json
- Reports generated by Nextflow: