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nf-core/fetchngs v1.0 - Steel Hippo
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@drpatelh drpatelh released this 08 Jun 15:04
· 1069 commits to master since this release
1.0
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[1.0] - 2021-06-08

Initial release of nf-core/fetchngs, created with the nf-core template.

Pipeline summary

Via a single file of ids, provided one-per-line the pipeline performs the following steps:

  1. Resolve database ids back to appropriate experiment-level ids and to be compatible with the ENA API
  2. Fetch extensive id metadata including direct download links to FastQ files via ENA API
  3. Download FastQ files in parallel via curl and perform md5sum check
  4. Collate id metadata and paths to FastQ files in a single samplesheet

Supported database ids

Currently, the following types of example identifiers are supported:

SRA ENA GEO
SRR11605097 ERR4007730 GSM4432381
SRX8171613 ERX4009132 GSE147507
SRS6531847 ERS4399630
SAMN14689442 SAMEA6638373
SRP256957 ERP120836
SRA1068758 ERA2420837
PRJNA625551 PRJEB37513
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