CWL Workflow: Build Bismark indices

Workflow: Build Bismark indices

Fetched 2025-01-24 09:15:42 GMT

Verified with cwltool version 3.1.20230201224320

Copy fasta_file file to the folder and run 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 input.

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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 (.fa or .fasta, or *.gz)	Reference genome FASTA file (.fa or .fasta, or *.gz). Includes all chromosomes

Steps

ID	Runs	Label	Doc
fasta_to_folder	bismark-index.cwl#fasta_to_folder/b489e687-5355-47ff-8bde-a2d9b581c08d (ExpressionTool)
prepare_indices	../tools/bismark-prepare-genome.cwl (CommandLineTool)		bismark_genome_preparation script generates indices using Bowtie2 aligners by default.

Outputs

ID	Type	Label	Doc
stderr_log	File	Bismark stderr log	Bismark generated stderr log
stdout_log	File	Bismark stdout log	Bismark generated stdout log
indices_folder	Directory	Bismark indices folder	Bismark generated indices folder