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.
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. |
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. |
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. |
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 Relationships
Used by
0 relationships
No components use this component.
Current component
tabix/tabix_querybiobox v0.5.0
Uses
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