bowtie2/bowtie2_inspect

Alignment

Indexing

Inspection

Description

Extract information from Bowtie2 index files.

By default, prints FASTA records of the indexed nucleotide sequences to
standard output. With -n, just prints names. With -s, just prints a summary of
the index parameters and sequences.

Type

bash_script

License

GPL-3.0

Keywords

Alignment

Indexing

Inspection

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bowtie2/bowtie2_inspect/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--index	string required	bt2 filename minus trailing .1.bt2/.2.bt2

Name

Type & Properties

--index

string

required

Outputs

Name	Type & Properties	Description
--output	file output	Save output to filename (default stdout)

Name

Type & Properties

--output

file

output

Output Options

Name	Type & Properties	Description
--summary	boolean_true	Print summary incl. ref names, lengths, index properties
--names	boolean_true	Print reference sequence names only
--across	integer	Number of characters across in FASTA output (default 60)
--verbose_inspect	boolean_true	Verbose output (for debugging)
--debug	boolean_true	Use the debug binary; slower, assertions enabled
--sanitized	boolean_true	Use sanitized binary; slower, uses ASan and/or UBSan
--verbose	boolean_true	Log the issued command

Name

Type & Properties

--summary

boolean_true

--names

boolean_true

--across

integer

--verbose_inspect

boolean_true

--debug

boolean_true

--sanitized

boolean_true

--verbose

boolean_true

Index Options

Name	Type & Properties	Description
--large_index	boolean_true	Force inspection of the 'large' index, even if a 'small' one is present

Name

Type & Properties

--large_index

boolean_true