kallisto/kallisto_index

kallisto

index

Description

Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.

Type

bash_script

License

BSD 2-Clause License

Keywords

kallisto

index

Links

Repository

Issues

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
index: "$id.$key.index.Kallisto_index"  
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_index/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input	file required	Path to a FASTA-file containing the transcriptome sequences, either in plain text or compressed (.gz) format.
--d_list	file	Path to a FASTA-file containing sequences to mask from quantification.

Name

Type & Properties

--input

file

required

--d_list

file

Output

Name	Type & Properties	Description
--index	file output

Name

Type & Properties

--index

file

output

Options

Name	Type & Properties	Description
--kmer_size	integer	Kmer length passed to indexing step of pseudoaligners (default: '31').
--make_unique	boolean_true	Replace repeated target names with unique names.
--aa	boolean_true	Generate index from a FASTA-file containing amino acid sequences.
--distiguish	boolean_true	Generate index where sequences are distinguished by the sequence names.
--min_size -m	integer	Length of minimizers (default: automatically chosen).
--ec_max_size -e	integer	Maximum number of targets in an equivalence class (default: no maximum).
--tmp -T	string	Path to a directory for temporary files.

Name

Type & Properties

--kmer_size

integer

--make_unique

boolean_true

--aa

boolean_true

--distiguish

boolean_true

--min_size

-m

integer

--ec_max_size

-e

integer

--tmp

-T

string