quantiseq-nf

Nextflow pipeline to run software quanTIseq in parallel to quantify immune cell content from RNA-seq data

Description

This Nextflow pipeline uses the singularity image of quanTIseq to launch the quanTIseq pipeline that performs immune cell quantification of 10 cell types from RNA-seq data. See https://icbi.i-med.ac.at/software/quantiseq/doc/ for general information about quanTIseq and the companion article Finotello, et al. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med. 2019;11:34. https://doi.org/10.1186/s13073-019-0638-6

Dependencies

1. Nextflow : for common installation procedures see the IARC-nf repository.
2. singularity

Input

Type	Description
--input_folder	a folder with RNA-seq fastq files

Parameters

• Optional

Name	Default value	Description
--output_folder	.	Output folder for results
--cpu	1	number of CPUs
--mem	2	memory
--fastq_ext	fq.gz	extension of fastq files
--suffix1	_1	suffix for second element of read files pair
--suffix2	_2	suffix for second element of read files pair
--image	null	singularity image

Note that if no singularity image is provided, the image is pulled from singularity hub. If the pipeline is reused frequently, it might be more efficient to pull the image manually with the command:

singularity pull quantiseq2.img IARCbioinfo/quantiseq-nf:v1.1

and then to provide the path to quantiseq2.img as a parameter.

Usage

nextflow run iarcbioinfo/quantiseq-nf -r v1.1 --input_folder input --output_folder output --image quantiseq2.img

Output

Type	Description
quanTIseq_cell_fractions_matrix.txt	a matrix with cell fractions (columns) for each sample (row)
quanTIseq_gene_tpm_matrix.txt	a matrix with gene counts (rows) for each sample (column)
intermediate_results/quantiseqResults_sample	a folder with quanTIseq results

For each sample, a folder is created in folder intermediate_results with the two quanTIseq output files (see https://icbi.i-med.ac.at/software/quantiseq/doc/ for details):

• quanTIseq_gene_tpm_sample.txt, the expression quantification table (in Transcripts Per Million or TPM) with a row for each of the 19424 annotated genes
• quanTIseq_cell_fractions_sample.txt, the table with the proportion of cells from each cell type (columns)

Directed Acyclic Graph

With default options

Contributions

Name	Email	Description
Tiffany Delhomme	Delhommet@student.iarc.fr	Developer
Nicolas Alcala*	AlcalaN@iarc.fr	Developer to contact for support