Fetch SRR Accession Workflow

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Data Import	Any Taxa	PHB v2.3.0	Yes	Sample-level

Fetch SRR Accession

This workflow retrieves the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. The primary inputs are BioSample IDs (e.g., SAMN00000000) or SRA Experiment IDs (e.g., SRX000000), which link to sequencing data in the SRA repository.

The workflow uses the fastq-dl tool to fetch metadata from SRA and specifically parses this metadata to extract the associated SRR accession and outputs the SRR accession.

Inputs

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
fetch_srr_metadata	sample_accession	String	SRA-compatible accession, such as a BioSample ID (e.g., "SAMN00000000") or SRA Experiment ID (e.g., "SRX000000"), used to retrieve SRR metadata.		Required
fetch_srr_metadata	cpu	Int	Number of CPUs allocated for the task.	2	Optional
fetch_srr_metadata	disk_size	Int	Disk space in GB allocated for the task.	10	Optional
fetch_srr_metadata	docker	String	Docker image for metadata retrieval.	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0	Optional
fetch_srr_metadata	memory	Int	Memory in GB allocated for the task.	8	Optional
version_capture	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0"	Optional
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional

Workflow Tasks

This workflow has a single task that performs metadata retrieval for the specified sample accession.

fastq-dl: Fetches SRR metadata for sample accession

When provided a BioSample accession or SRA experiment ID, 'fastq-dl' collects metadata and returns the appropriate SRR accession.

fastq-dl Technical Details

	Links
Task	Task on GitHub
Software Source Code	fastq-dl Source
Software Documentation	fastq-dl Documentation
Original Publication	fastq-dl: A fast and reliable tool for downloading SRA metadata

Outputs

Variable	Type	Description
srr_accession	String	The SRR accession's associated with the input sample accession.
fetch_srr_accession_version	String	The version of the fetch_srr_accession workflow.
fetch_srr_accession_analysis_date	String	The date the fetch_srr_accession analysis was run.

References

Valieris, R. et al., "fastq-dl: A fast and reliable tool for downloading SRA metadata." Bioinformatics, 2021.