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nf-core/fetchngs v1.4 - Platinum Hawk
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@drpatelh drpatelh released this 09 Nov 15:28
· 872 commits to master since this release
1.4
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[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
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