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Releases: nf-core/fetchngs

nf-core/fetchngs v1.3 - Lead Python

15 Sep 16:31
@drpatelh drpatelh
1.3
2d593fb
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nf-core/fetchngs v1.3 - Lead Python

[1.3] - 2021-09-15

Enhancements & fixes

  • Replaced Python requests with urllib to fetch ENA metadata

Software dependencies

Dependency Old version New version
python 3.8.3 3.9.5
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nf-core/fetchngs v1.2 - Silver Fox

28 Jul 08:25
@drpatelh drpatelh
1.2
8c00805
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nf-core/fetchngs v1.2 - Silver Fox

[1.2] - 2021-07-28

Enhancements & fixes

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nf-core/fetchngs v1.1 - Titanium Toad

22 Jun 10:14
@drpatelh drpatelh
1.1
3bd6ea5
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nf-core/fetchngs v1.1 - Titanium Toad

[1.1] - 2021-06-22

Enhancements & fixes

  • [#12] - Error when using singularity - /etc/resolv.conf doesn't exist in container
  • Added --sample_mapping_fields parameter to create a separate id_mappings.csv and multiqc_config.yml with selected fields that can be used to rename samples in general and in MultiQC
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nf-core/fetchngs v1.0 - Steel Hippo

08 Jun 15:04
@drpatelh drpatelh
1.0
4611da4
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nf-core/fetchngs v1.0 - Steel Hippo

[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
Assets 2
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