qualimap

Description

RNA-seq QC analysis using the qualimap

Type

bash_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_dir: "$id.$key.output_dir"  
output_pdf: "$id.$key.output_pdf"  
output_format: [ "html" ]  
pr_bases: [ 100 ]  
tr_bias: [ 1000 ]  
algorithm: [ "uniquely-mapped-reads" ]  
sequencing_protocol: [ "non-strand-specific" ]  
java_memory_size: [ "4G" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.1.1 \  
  -main-script target/nextflow/qualimap/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	path to input mapping file in BAM format.
--gtf	file required	path to annotations file in Ensembl GTF format.

Name

Type & Properties

--input

file

required

--gtf

file

required

Output

Name	Type & Properties	Description
--output_dir	file output	path to output directory for raw data and report.
--output_pdf	file output	path to output file for pdf report.
--output_format	string	Format of the output report (PDF or HTML, default is HTML)

Name

Type & Properties

--output_dir

file

output

--output_pdf

file

output

--output_format

string

Optional

Name	Type & Properties	Description
--pr_bases	integer	Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default = 100).
--tr_bias	integer	Number of top highly expressed transcripts to compute 5'-3' bias (default = 1000).
--algorithm	string	Counting algorithm (uniquely-mapped-reads (default) or proportional).
--sequencing_protocol	string	Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).
--paired	boolean_true	Setting this flag for paired-end experiments will result in counting fragments instead of reads.
--sorted	boolean_true	Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis.
--java_memory_size	string	maximum Java heap memory size, default = 4G.

Name

Type & Properties

--pr_bases

integer

--tr_bias

integer

--algorithm

string

--sequencing_protocol

string

--paired

boolean_true

--sorted

boolean_true

--java_memory_size

string