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.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--index | file required | Directory containing the bowtie2 index files (`.1.bt2`, `.2.bt2`, `.3.bt2`, `.4.bt2`, `.rev.1.bt2` and `.rev.2.bt2`, or their `.bt2l` equivalents for a large index), as produced by `bowtie2_build`. When the directory holds a single index, its prefix is derived from the contents of the directory; when it holds more than one, use `--index_prefix` to select one. |
--index_prefix | string | Prefix of the index to use from the `--index` directory, that is, the name the index files share with their extensions (`.1.bt2`, `.2.bt2`, `.3.bt2`, `.4.bt2`, `.rev.1.bt2` and `.rev.2.bt2`, or their `.bt2l` equivalents) removed. Required when the directory contains more than one index; when omitted, the single index present in the directory is used. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Save output to filename (default stdout) |
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 |
Index Options
Name | Type & Properties | Description |
|---|---|---|
--large_index | boolean_true | Force inspection of the 'large' (`.bt2l`) index, even if a 'small' (`.bt2`) one is present. Fails if `--index` contains no large index. When not set, a small index is preferred and a large one is used when that is all the index directory contains. |
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 v0.5.0 \
-main-script target/nextflow/bowtie2/bowtie2_inspect/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
bowtie2/bowtie2_inspectbiobox v0.5.0
Uses
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