Workflow: Build Bowtie indices
Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
genome | String | Genome type |
Genome type, such as mm10, hg19, hg38, etc |
fasta_file | File [FASTA] | Reference genome FASTA file |
Reference genome FASTA file. Includes all chromosomes |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bowtie_build |
../tools/bowtie-build.cwl
(CommandLineTool)
|
Tool runs bowtie-build Not supported parameters: -c - reference sequences given on cmd line (as <seq_in>) |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
stderr_log | File | Bowtie stderr log |
Bowtie generated stderr log |
stdout_log | File | Bowtie stdout log |
Bowtie generated stdout log |
indices_folder | Directory | Bowtie indices |
Bowtie generated indices folder |
Permalink:
https://w3id.org/cwl/view/git/480e99a4bb3046e0565113d9dca294e0895d3b0c/workflows/bowtie-index.cwl