modules/cellbender_removebackground

Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data

single-cellscRNA-seqambient RNA removal

https://github.com/nf-core/modules/[...]/modules/nf-core/cellbender/removebackground

Description

Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`h5ad:file`

AnnData file containing unfiltered data (with empty droplets)

*.h5ad

Output

name:type

description

pattern

`h5`

`meta:map`

Groovy Map containing sample information

`${prefix}.h5:file`

Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes.

*.h5

`filtered_h5`

`meta:map`

Groovy Map containing sample information

`${prefix}_filtered.h5:file`

Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.

*.h5

`posterior_h5`

`meta:map`

Groovy Map containing sample information

`${prefix}_posterior.h5:file`

The full posterior probability of noise counts. This is not normally used downstream.

*.h5

`barcodes`

`meta:map`

Groovy Map containing sample information

`${prefix}_cell_barcodes.csv:file`

CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | Barcodes are written in plain text. This information is also contained in each of the above outputs, | but is included as a separate output for convenient use in certain downstream applications.

*.csv

`metrics`

`meta:map`

Groovy Map containing sample information

`${prefix}_metrics.csv:file`

Metrics describing the run, potentially to be used to flag problematic runs | when using CellBender as part of a large-scale automated pipeline.

*.csv

`report`

`meta:map`

Groovy Map containing sample information

`${prefix}_report.html:file`

HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.

*.html

`pdf`

`meta:map`

Groovy Map containing sample information

`${prefix}.pdf:file`

PDF file that provides a standard graphical summary of the inference procedure.

*.pdf

`log`

`meta:map`

Groovy Map containing sample information

`${prefix}.log:file`

Log file produced by the cellbender remove-background run.

*.log

`checkpoint`

`meta:map`

Groovy Map containing sample information

`ckpt.tar.gz:file`

Checkpoint file which contains the trained model and the full posterior.

*.ckpt

`versions`

`versions.yml:file`

File containing software version

versions.yml

Tools

cellbender
BSD-3-Clause

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

cellbender.readthedocs.io/en/latest https://github.com/broadinstitute/CellBender