Outputs

  1. Layout
  2. CellBender output
  3. QC report
  4. Versions
  5. How files are published

Layout

Everything is written to --outdir (default results/):

results/
├── raw/<id>/                       data downloaded from iRODS (with --on_irods)
├── cellbender/<id>/                CellBender output for each sample
├── index/
│   ├── cellbender.csv              id,path of every CellBender output folder
│   └── raw.csv                     id,path of every iRODS download (empty without --on_irods)
├── qc_report/
│   ├── cellbender_qc_summary.tsv   one row per sample, most problematic samples first
│   ├── cellbender_qc_report.pdf    summary table, training curves, cell calling, latent PCA, soup, gene removal
│   ├── multiqc_report.html         the same QC as an interactive HTML report
│   ├── multiqc_data/               data behind the MultiQC report
│   └── multiqc/                    MultiQC input files
└── versions.yml                    software versions

Run reports from Nextflow (timeline, resource report, trace) go to execution-reports/ in the launch folder, not to --outdir.

CellBender output

Each cellbender/<id>/ folder holds what cellbender remove-background wrote for that sample:

File 0.2 0.3 Contents
cellbender.h5 ✓ ✓ Corrected counts for all analysed droplets, plus latent variables
cellbender_filtered.h5 ✓ ✓ Corrected counts for droplets with cell probability > 0.5
cellbender_cell_barcodes.csv ✓ ✓ Barcodes with cell probability > 0.5
cellbender.pdf ✓ ✓ CellBender’s own summary plots
cellbender.log ✓ ✓ CellBender’s log, read by the QC step
cellbender_metrics.csv   ✓ Run metrics
cellbender_report.html   ✓ CellBender’s own HTML report, with warnings
cellbender_posterior.h5   ✓ Posterior of noise counts

For downstream analysis use cellbender_filtered.h5. The CellBender documentation describes each file in detail.

QC report

qc_report/ is described column by column in QC report.

Versions

versions.yml records the version of every tool used in the run:

"CELLBENDER:CELLBENDER_REMOVEBACKGROUND_V03":
    cellbender: 0.3.2
"CELLBENDER_QC":
    python: 3.10.12
    h5py: 3.14.0
    matplotlib: 3.10.3
"MULTIQC":
    multiqc: 1.35

How files are published

Outputs are copied out of nf-work/ by default. --publish_mode (hidden, see --help --showHidden) also accepts symlink, link, rellink, copyNoFollow and move.

With symlink or rellink, the results point into nf-work/: deleting it then deletes the results too.