CWL Workflow: Build Bowtie indices

Workflow: Build Bowtie indices

Fetched 2025-02-26 11:17:27 GMT

Verified with cwltool version 3.1.20230201224320

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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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