Viash Hub

Description

Map a list of FASTQ files (one for each well) to a reference genome and generate count matrices.
Sometimes counts from different FASTQ files need to be concatenated. This is done bases on the sample_id:
if the sample ID of the two plates are identical, the FASTQ files will we joined before mapping.

Input arguments

Name	Type & Properties	Description
--input_r1	file required multiple	Forward reads in FASTQ format.
--input_r2	file required multiple	Reverse reads in FASTQ format.
--barcodesFasta	file required
--umi_length	integer	Length of the UMI sequences
--genomeDir	file required
--annotation	file required
--sample_id	string	Sample ID for the provided input files. If not provided, the value of --id will be used. Input files will allways be demultiplexed separately, but the FASTQs for wells with matching sample IDs will be concatenated before mapping.
--run_params	file	file with the processing parameters

Name

Type & Properties

--input_r1

file

required

multiple

--input_r2

file

required

multiple

--barcodesFasta

file

required

--umi_length

integer

--genomeDir

file

required

--annotation

file

required

--sample_id

string

--run_params

file

Output arguments

Name	Type & Properties	Description
--star_output	file required multiple output	Output from mapping with STAR
--nrReadsNrGenesPerChrom	file required output
--star_qc_metrics	file required output
--eset	file required output
--f_data	file required output
--p_data	file required output
--html_report	file required output

Name

Type & Properties

--star_output

file

required

multiple

output

--nrReadsNrGenesPerChrom

file

required

output

--star_qc_metrics

file

required

output

--eset

file

required

output

--f_data

file

required

output

--p_data

file

required

output

--html_report

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
umi_length: [ 10 ]  
star_output: "$id.$key.star_output._*"  
nrReadsNrGenesPerChrom: "$id.$key.nrReadsNrGenesPerChrom"  
star_qc_metrics: "$id.$key.star_qc_metrics"  
eset: "$id.$key.eset"  
f_data: "$id.$key.f_data"  
p_data: "$id.$key.p_data"  
html_report: "$id.$key.html_report"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.15.0-rc.2 \  
  -main-script target/nextflow/workflows/well_fastqs_to_esets/main.nf \  
  -params-file params.yaml