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nf-core/fetchngs

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Pipeline to fetch metadata and raw FastQ files from public databases

Is nf-core/fetchngs beginner-friendly?

The maintainers of nf-core/fetchngs usually reply to a pull request within 1 day. 2 beginner-friendly issues are open now.

Stars
202
Forks
96
Open beginner issues
2
Indexed issues
41
Avg merge
6h 36m
Merged PRs (30d)
4
Dominant language
Nextflow
License
MIT
Last GitHub push
Oct 8, 2026
Latest indexed
Sep 19, 2026
Contributing guide
Code of conduct
Beginner labels
No beginner labels indexed

How to contribute to nf-core/fetchngs

  1. Read the contributing guide first: it says how the maintainers want changes proposed, tested and reviewed.
  2. The project ships a dev container: open it in Codespaces to get a working environment in your browser.
  3. Read its code of conduct: it covers issues and pull requests as well as chat.
  4. Pick one of the 2 open beginner-friendly issues below and comment that you want to work on it before you start.
Beginner friendly Everything
Open All

Issues somebody may already be working on are listed last. List everything by date

  • fastq-dl miss publish mode specification
    Open
    • Is something wrong?
    bug

    Difficulty 1/5 Under an hour Newbie friendliness 78/100

    nf-core/fetchngs#416 · 1 comment ·

    Maintainers usually reply within 1 day

  • 1.13.0: `--nf_core_pipeline mag` emits a samplesheet mag rejects (empty `group`, `fastq_1/2` instead of `short_reads_1/2`)
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 74/100

    nf-core/fetchngs#401 · 1 reaction ·

    Maintainers usually reply within 1 day

  • Replace deprecated cgi module in sra_ids_to_runinfo
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 74/100

    nf-core/fetchngs#390 ·

    Maintainers usually reply within 1 day

  • restore mkfg file from CUSTOM_SRATOOLSNCBISETTINGS / FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    nf-core/fetchngs#377 ·

    Maintainers usually reply within 1 day

  • fetchngs 1.12 produces empty runinfo.tsv because ENA no longer accepts parent_study
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 75/100

    nf-core/fetchngs#372 · 1 comment ·

    Maintainers usually reply within 1 day

  • SRA tools fetching fails on AWS, fixable by updating sra-toolkit version
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 42/100

    nf-core/fetchngs#364 ·

    Maintainers usually reply within 1 day

  • Fetching from the European Genome-Phenome Archive
    Open
    • Is something wrong?
    enhancement

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    nf-core/fetchngs#360 ·

    Maintainers usually reply within 1 day

  • ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)'
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    nf-core/fetchngs#351 ·

    Maintainers usually reply within 1 day

  • ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)'
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 28/100

    nf-core/fetchngs#346 · 1 comment ·

    Maintainers usually reply within 1 day

  • Add support for cloud platform
    Open
    • Is something wrong?
    enhancement

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    nf-core/fetchngs#345 · 1 comment ·

    Maintainers usually reply within 1 day

  • Add xsra support
    Open
    • Is something wrong?
    enhancement

    Difficulty 5/5 Over a week Newbie friendliness 20/100

    nf-core/fetchngs#344 ·

    Maintainers usually reply within 1 day

  • Partition error on SLURM only with fetchngs -
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    nf-core/fetchngs#343 ·

    Maintainers usually reply within 1 day

  • Fetchngs fails with error: terminated with an error exit status (1) -- Execution is retried (1)
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    nf-core/fetchngs#342 · 1 comment ·

    Maintainers usually reply within 1 day

  • fetchngs test fails
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 20/100

    nf-core/fetchngs#336 · 2 reactions ·

    Maintainers usually reply within 1 day

  • fasterq-dump => disk: local-ssd
    Open
    • Is something wrong?
    enhancement

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    nf-core/fetchngs#332 · 3 comments ·

    Maintainers usually reply within 1 day

  • Incorrect MD5 checksums being used for some files
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 38/100

    nf-core/fetchngs#331 ·

    Maintainers usually reply within 1 day

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

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#328 · 3 comments ·

    Maintainers usually reply within 1 day

  • Incorrect fastq paths in scRNA-seq sample sheet
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 32/100

    nf-core/fetchngs#326 · 1 reaction ·

    Maintainers usually reply within 1 day

  • Update some modeles for TES compliance
    May be free again Open
    • Is something wrong?
    bug

    nf-core/fetchngs#318 · 1 assignee ·

    Maintainers usually reply within 1 day

  • SRATOOLS_FASTERQDUMP failing due to missing fastq file
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#317 · 11 comments ·

    Maintainers usually reply within 1 day

  • Support for CNBG
    Open
    • Is something wrong?
    enhancement

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    nf-core/fetchngs#315 ·

    Maintainers usually reply within 1 day

  • DDBJ study ids (DRP123456) do not map correctly
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 45/100

    nf-core/fetchngs#314 ·

    Maintainers usually reply within 1 day

  • Support for GSA accessions
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#313 · 2 reactions ·

    Maintainers usually reply within 1 day

  • SRA file links deprecated
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    nf-core/fetchngs#301 · 3 comments ·

    Maintainers usually reply within 1 day

  • wget host address error
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 45/100

    nf-core/fetchngs#291 · 13 comments · 2 reactions ·

    Maintainers usually reply within 1 day

  • Merge technical replicates (SRR1 + SRR2 -> SRX)
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 45/100

    nf-core/fetchngs#270 ·

    Maintainers usually reply within 1 day

  • Add ability to download more than 2 FastQ files via FTP and Aspera
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#260 · 3 comments ·

    Maintainers usually reply within 1 day

  • check out extensions for input files
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    nf-core/fetchngs#256 · 3 comments ·

    Maintainers usually reply within 1 day

  • Use nf-test for input validation
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    nf-core/fetchngs#254 ·

    Maintainers usually reply within 1 day

  • FEAT: Pass scientific name as input to download the data
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    nf-core/fetchngs#235 ·

    Maintainers usually reply within 1 day

  • Add compatibility with sarek samplesheet
    Open
    • Is something wrong?
    enhancement

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    nf-core/fetchngs#196 ·

    Maintainers usually reply within 1 day

  • Deal with accessions with non-existing files
    May be free again Open
    • Is something wrong?
    enhancement

    nf-core/fetchngs#139 · 7 comments · 1 assignee ·

    Maintainers usually reply within 1 day

  • eutils rate limits exceeded (with relatively small input set of accessions)
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    nf-core/fetchngs#117 · 4 comments · 1 reaction ·

    Maintainers usually reply within 1 day

  • Use ffq to fetch id metadata
    May be free again Open
    • Is something wrong?
    enhancement

    nf-core/fetchngs#110 · 1 assignee ·

    Maintainers usually reply within 1 day

  • Can SRA responses be trapped and reported in a user-friendly manner?
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#108 · 1 comment ·

    Maintainers usually reply within 1 day

  • add --save_merged_fastq for merging technical repeats to fetchngs
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#95 · 5 comments · 1 reaction ·

    Maintainers usually reply within 1 day

  • Allow a prepared ENA metadata samplesheet as input
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    nf-core/fetchngs#77 · 1 comment ·

    Maintainers usually reply within 1 day

  • Check if running offline
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 32/100

    nf-core/fetchngs#18 · 1 comment ·

    Maintainers usually reply within 1 day

  • SRA_FASTQ_FTP requests 12 GB / 2 CPUs (up to 36 GB / 6 CPUs on retry) for a download that uses ~15 MB
    Possibly taken Open
    • Is something wrong?
    bug

    Difficulty 2/5 1-3 hours Newbie friendliness 78/100

    nf-core/fetchngs#407 ·

    Maintainers usually reply within 1 day

  • Add direct AWS download method
    Possibly taken Open
    • Is something wrong?
    enhancement

    Difficulty 3/5 1-2 days Newbie friendliness 48/100

    nf-core/fetchngs#354 · 1 comment · 1 reaction ·

    Maintainers usually reply within 1 day

  • SRAtools download seems to insert paired-end suffix into workdir path
    Possibly taken Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    nf-core/fetchngs#221 · 7 comments ·

    Maintainers usually reply within 1 day

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