Publication dateMar 9, 2022
Confidentiality public Public
timer
11 minutes, 9 seconds
Typing name : TASK.gws_omix.download_sra_ena Brick : gws_omix Download FASTQ files from SRA or ENA repositories.
Python wrapper around fastq-dl (https://github.com/rpetit3/fastq-dl) that downloads FASTQ files for one or more accessions
(ENA or SRA), then merges/creates a fastq-run-info.tsv summary and keeps only key columns.
Inputs:
accession (str): One or more accession IDs separated by commas
(e.g. "SRX1,SRX2,PRJNA...,SRR...")
provider (str): "ena" or "sra" (default/fallback: "ena")
cpus (int): number of CPU threads (default: 2)
Outputs:
- Directory containing downloaded FASTQ file(s) (e.g. *.fastq.gz)
(all saved in the same folder)
- fastq-run-info.tsv table listing all runs resolved under all input accessions
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Output
FASTQ folder
All downloaded FASTQ(.gz)/SRA files.
FASTQ run metadata (TSV)
Normalized ENA/SRA run info.
settings
Configuration
Accession(s) comma-separated (PRJNA..., SRP..., SRX..., SRR...)
Type : stringProvider: ena or sra
Type : stringAllowed values : sra
ena
Default value : sraCPUs for fastq-dl (esp. for SRA)
Type : intDefault value : 2Technical bricks to reuse or customize Have you developed a brick?
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