Build Bowtie 2 index

Builds a Bowtie 2 index directory from a FASTA reference.

Step type:: Utility step

Run this step

ASOkai run --step build-bowtie2-index --config-file ./config.yaml

Example configuration for this step:

datadir: ./data

Parameters

These scalar configuration values are passed to this step.

Configuration path	Details
`parameters.bowtie2.large_index`	Accepted value: boolean Requirement: Optional Description: Force the large .bt2l index format.
`parameters.bowtie2.offrate`	Accepted value: integer or null; minimum: 0 Requirement: Optional Description: Suffix-array sampling rate.
`parameters.bowtie2.packed`	Accepted value: boolean Requirement: Optional Description: Use packed representation while building.

Inputs

An input with a fixed producer uses that output by default. A selected run can instead link a named output or supply an existing path. The input’s path override in config.yaml also selects an existing file. External paths are validated against the input’s file contract.

File input	Details
`reference`	Shared config source: `steps.build-bowtie2-index.inputs.reference.path` or `steps.build-bowtie2-index.inputs.reference.from` Format: plain FASTA reference Description: Plain FASTA reference to index.

Example path-override configuration:

steps:
  build-bowtie2-index:
    inputs:
      reference:
        path: /path/to/reference.fa

Resources

Configurable resources use the first value in the resolution order shown below.

Resource setting	Details
`n_workers`	Step override: `resources.build-bowtie2-index.n_workers` Shared default: `resources.default.n_workers` Built-in fallback: 1 Accepted value: integer; minimum: 1 Description: Number of workers allocated to a step that supports parallel execution.
`memory_mb`	Step override: `resources.build-bowtie2-index.memory_mb` Shared default: `resources.default.memory_mb` Built-in fallback: 4096 Accepted value: integer; minimum: 1 Description: Memory in mebibytes allocated to this step.

Outputs

File output paths are relative to datadir. Braced names are replaced with the corresponding parameter values.

File outputs

File output	Details
`index`	Format: Bowtie 2 index directory Description: Directory containing the six Bowtie 2 index files. Path template: `{assembly}/{source}/{release}/indexes/bowtie2/index.offrate{offrate}.large{large}.packed{packed}` Example path: `GRCh38/ensembl/114/indexes/bowtie2/index.offrateauto.largeFalse.packedFalse`

Note

This step invokes the third-party bowtie2-build executable. Bowtie 2 is GPLv3 software; ASOkai does not distribute or link against it. Install the executable through the supplied Conda environment.

Supply any plain FASTA reference. The index destination includes the Bowtie 2 build options. In the default signature validation mode, its receipt records the selected FASTA input, so changing the reference causes a rebuild at the same destination.

To index a target gene, name an instantiate-target-gene task run target_gene and link reference to its fasta output:

runs:
  - task: instantiate-target-gene
    id: target_gene
  - step: build-bowtie2-index
    inputs:
      reference:
        from: run.target_gene.fasta

On the CLI, select an existing FASTA with:

ASOkai run --no-config \
  --step build-bowtie2-index --input reference=path:/path/to/reference.fa

To link a named producer in the same CLI selection, use --input reference=from:run.target_gene.fasta after the index step.