Issues

• 1.13.0: --nf_core_pipeline mag emits a samplesheet mag rejects (empty group, fastq_1/2 instead of short_reads_1/2)

  nf-core/fetchngs#401 · Filter by author vagkaratzas opened on Sep 15, 2026

• Replace deprecated cgi module in sra_ids_to_runinfo

  bug
  nf-core/fetchngs#390 · Filter by author maxulysse opened on Sep 10, 2026

• restore mkfg file from CUSTOM_SRATOOLSNCBISETTINGS / FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS

  bug
  nf-core/fetchngs#377 · Filter by author maxulysse opened on Aug 10, 2026

• fetchngs 1.12 produces empty runinfo.tsv because ENA no longer accepts parent_study

  bug
  nf-core/fetchngs#372 · Filter by author KristinaGagalova opened on Aug 7, 2026
  1

• SRA tools fetching fails on AWS, fixable by updating sra-toolkit version

  bug
  nf-core/fetchngs#364 · Filter by author ivirshup opened on Mar 20, 2026

• Fetching from the European Genome-Phenome Archive

  enhancement
  nf-core/fetchngs#360 · Filter by author UtaHar opened on Oct 23, 2025

• Add direct AWS download method

  enhancement
  nf-core/fetchngs#354 · Filter by author tanaes opened on Aug 14, 2025

• ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)'

  bug
  nf-core/fetchngs#351 · Filter by author JuriBeretta opened on Jul 24, 2025

• ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)'

  bug
  nf-core/fetchngs#346 · Filter by author Luke-ebbis opened on May 12, 2025 · 1.13.0
  1

• Add support for cloud platform

  enhancement
  nf-core/fetchngs#345 · Filter by author Zhenghongc opened on May 8, 2025
  1

• Add xsra support

  enhancement
  Enhancement

  nf-core/fetchngs#344 · Filter by author edmundmiller opened on May 1, 2025

• Partition error on SLURM only with fetchngs -

  bug
  nf-core/fetchngs#343 · Filter by author DollyCM opened on Apr 9, 2025 · 1.13.0

• Fetchngs fails with error: terminated with an error exit status (1) -- Execution is retried (1)

  bug
  nf-core/fetchngs#342 · Filter by author kanekalla opened on Mar 26, 2025
  1

• fetchngs test fails

  nf-core/fetchngs#336 · Filter by author mjfi2sb3 opened on Feb 6, 2025 · 1.13.0

• fasterq-dump => disk: local-ssd

  enhancement
  nf-core/fetchngs#332 · Filter by author nick-youngblut opened on Jan 11, 2025 · 1.13.0
  3

• Incorrect MD5 checksums being used for some files

  bug
  nf-core/fetchngs#331 · Filter by author tanaes opened on Jan 9, 2025 · 1.13.0

• 1.11.0 works while 1.12.0 fails for apptainer+wget ( wget: unable to resolve host address 'ftp.sra.ebi.ac.uk' )

  bug
  nf-core/fetchngs#328 · Filter by author lindenb opened on Dec 9, 2024 · 1.13.0
  3

• Incorrect fastq paths in scRNA-seq sample sheet

  bug
  nf-core/fetchngs#326 · Filter by author huldash opened on Nov 29, 2024

• Update some modeles for TES compliance

  bug
  nf-core/fetchngs#318 · Filter by author vsmalladi opened on Sep 13, 2024 · 1.13.0
  

• SRATOOLS_FASTERQDUMP failing due to missing fastq file

  bug
  nf-core/fetchngs#317 · Filter by author edg1983 opened on Jul 24, 2024
  11

• Support for CNBG

  enhancement
  nf-core/fetchngs#315 · Filter by author nathaniel-mahieu opened on Jul 1, 2024

• DDBJ study ids (DRP123456) do not map correctly

  bug
  nf-core/fetchngs#314 · Filter by author awalsh17 opened on Jul 1, 2024

• Support for GSA accessions

  enhancement
  nf-core/fetchngs#313 · Filter by author millerh1 opened on May 30, 2024

• SRA file links deprecated

  bug
  nf-core/fetchngs#301 · Filter by author tiendu opened on Mar 7, 2024 · 1.13.0
  3

• wget host address error

  bug
  nf-core/fetchngs#291 · Filter by author mniederhuber opened on Feb 23, 2024 · 1.13.0
  13