CWL Workflow: Generate genome indices for Bismark

Workflow: Generate genome indices for Bismark

Fetched 2023-01-04 15:32:01 GMT

Verified with cwltool version 3.1.20221201130942

Run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome folder name.

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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_label	String (Optional)	Genome label	Genome label is used by web-ui to show label
genome_folder	Directory	Folder with the genome FASTA files	Folder with the genome FASTA files (.fa, .fasta)
genome_details	String (Optional)	Genome details	Genome details
genome_description	String (Optional)	Genome description	Genome description is used by web-ui to show description

Steps

ID	Runs	Label	Doc
prepare_indices	../tools/bismark-prepare-genome.cwl (CommandLineTool)		bismark_genome_preparation script generates indices using Bowtie2 aligners by default.

Outputs

ID	Type	Label	Doc
indices_folder	Directory	Bismark indices folder	Bismark generated indices folder