kallisto/kallisto_quant

kallisto

quant

pseudoalignment

Description

Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Type

bash_script

License

BSD 2-Clause License

Keywords

kallisto

quant

pseudoalignment

Links

Repository

Issues

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_dir: "$id.$key.output_dir"  
log: "$id.$key.log"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/kallisto/kallisto_quant/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required multiple	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
--index -i	file required	Kallisto genome index.

Name

Type & Properties

--input

file

required

multiple

--index

-i

file

required

Output

Name	Type & Properties	Description
--output_dir -o	file required output	Directory to write output to.
--log	file output	File containing log information from running kallisto quant

Name

Type & Properties

--output_dir

-o

file

required

output

--log

file

output

Options

Name	Type & Properties	Description
--single	boolean_true	Single end mode.
--single_overhang	boolean_true	Include reads where unobserved rest of fragment is predicted to lie outside a transcript.
--fr_stranded	boolean_true	Strand specific reads, first read forward.
--rf_stranded	boolean_true	Strand specific reads, first read reverse.
--fragment_length -l	double	The estimated average fragment length.
--sd -s	double	The estimated standard deviation of the fragment length (default: -l, -s values are estimated from paired end data, but are required when using --single).
--plaintext	boolean_true	Output plaintext instead of HDF5.
--bootstrap_samples -b	integer	Number of bootstrap samples to draw. Default: '0'
--seed	integer	Random seed for bootstrap. Default: '42'

Name

Type & Properties

--single

boolean_true

--single_overhang

boolean_true

--fr_stranded

boolean_true

--rf_stranded

boolean_true

--fragment_length

-l

double

--sd

-s

double

--plaintext

boolean_true

--bootstrap_samples

-b

integer

--seed

integer