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nf-core/fetchngs: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unpublished Version / DEV]

Enhancements & fixes

[1.5] - 2021-12-01

  • Finish porting the pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
    • Bump minimum Nextflow version from 21.04.0 -> 21.10.3
    • Removed --publish_dir_mode as it is no longer required for the new syntax

Enhancements & fixes

[1.4] - 2021-11-09

Enhancements & fixes

  • Convert pipeline to updated Nextflow DSL2 syntax for future adoption across nf-core
  • Added a workflow to download FastQ files and to create samplesheets for ids from the Synapse platform hosted by Sage Bionetworks.
  • SRA identifiers not available for direct download via the ENA FTP will now be downloaded via sra-tools.
  • Added --force_sratools_download parameter to preferentially download all FastQ files via sra-tools instead of ENA FTP.
  • Correctly handle errors from SRA identifiers that do not return metadata, for example, due to being private.
  • Retry an error in prefetch via bash script in order to allow it to resume interrupted downloads.
  • Name output FastQ files by {EXP_ACC}_{RUN_ACC}*fastq.gz instead of {EXP_ACC}_{T*}*fastq.gz for run id provenance
  • [#46] - Bug in sra_ids_to_runinfo.py
  • Added support for DDBJ ids. See examples below:
DDBJ
PRJDB4176
SAMD00114846
DRA008156
DRP004793
DRR171822
DRS090921
DRX162434

[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

[1.2] - 2021-07-28

Enhancements & fixes

[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

[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