Workflow: prefetch_fastq.cwl

Fetched 2024-10-11 02:39:50 GMT

Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd

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Inputs

ID Type Title Doc
sra_accession String

Steps

ID Runs Label Doc
prefetch
prefetch.cwl (CommandLineTool)

Tool runs prefetch from NCBI SRA toolkit

fastq_dump
fastq_dump.cwl (CommandLineTool)

Tool runs fastq-dump from NCBI SRA toolkit Supports only file inputs. Output file names are formed on the base of `sra_file` input basename.

rename_fastq1
../util/rename.cwl (ExpressionTool)

Also consider https://www.commonwl.org/user_guide/misc/#rename-an-input-file or https://www.commonwl.org/user_guide/misc/#rename-an-output-file

Outputs

ID Type Label Doc
fastq_files File[] [FASTQ-illumina]
fastq_file_1 File [FASTQ-illumina]
fastq_file_2 File (Optional) [FASTQ-illumina]
Permalink: https://w3id.org/cwl/view/git/82b291f7d205024b2db7d4106a448c8a65855439/bio-cwl-tools/sratoolkit/prefetch_fastq.cwl