tabix/tabix_query

query

tabix

htslib

vcf

bed

gff

Description

Query a tabix/CSI-indexed, BGZF block-compressed file by region or list its
chromosomes.

Type

bash_script

License

MIT/Expat

Keywords

query

tabix

htslib

vcf

bed

gff

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.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/tabix/tabix_query/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	BGZF block-compressed file to query.
--index	file required	Index for `--input` (`.tbi`, `.csi`, `.bai`, or `.crai`), as produced by `tabix`.
--region	string multiple	One or more regions to query, e.g. `chr1:1000-2000`.
--regions_file	file	BED or tab-delimited file listing regions to restrict output to (index-jumps to each region).
--targets_file	file	Like `--regions_file`, but streams through the input rather than index-jumping to each region.

Name

Type & Properties

--input

file

required

--index

file

required

--region

string

multiple

--regions_file

file

--targets_file

file

Outputs

Name	Type & Properties	Description
--output	file required output	List of chromosome names in the file if `--list_chroms` is set, otherwise lines matching the query regions.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--print_header	boolean_true	Also print the header lines in output.
--only_header -H	boolean_true	Print only the header lines.
--list_chroms -l	boolean_true	List chromosome names from the index. If this is set, the output is a list of chromosome names rather than lines matching the query regions.
--unique -u	boolean_true	Only output each region once, even if overlapping. Cannot be combined with `--separate_regions`.
--separate_regions	boolean_true	Separate the output by corresponding region. Cannot be combined with `--unique`.
--cache	integer	BGZF block cache size in megabytes (`0` disables it). Default: 10.
--verbosity	integer	Logging verbosity. Default: 3.
--skip_index_download -D	boolean_true	Do not download the index file for remote inputs.

Name

Type & Properties

--print_header

boolean_true

--only_header

-H

boolean_true

--list_chroms

-l

boolean_true

--unique

-u

boolean_true

--separate_regions

boolean_true

--cache

integer

--verbosity

integer

--skip_index_download

-D

boolean_true