nf-core/fetchngs

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Pipeline to fetch metadata and raw FastQ files from public databases

Stars: 202
Forks: 93
Open beginner issues: 0
Indexed issues: 39
Avg merge: 1d 18m
Merged PRs (30d): 15

Dominant language: Nextflow
License: MIT
Last GitHub push: Sep 15, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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39 open issues indexed

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

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

nf-core/fetchngs#401 · 1 reaction · Opened Sep 15, 2026
Replace deprecated cgi module in sra_ids_to_runinfo Open

bug

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

nf-core/fetchngs#390 · Opened Sep 10, 2026
restore mkfg file from CUSTOM_SRATOOLSNCBISETTINGS / FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS Open

bug

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

nf-core/fetchngs#377 · Opened Aug 10, 2026
fetchngs 1.12 produces empty runinfo.tsv because ENA no longer accepts parent_study Open

bug

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

nf-core/fetchngs#372 · 1 comment · Opened Aug 7, 2026
SRA tools fetching fails on AWS, fixable by updating sra-toolkit version Open

bug

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

nf-core/fetchngs#364 · Opened Mar 20, 2026
Fetching from the European Genome-Phenome Archive Open

enhancement

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

nf-core/fetchngs#360 · Opened Oct 23, 2025
Add direct AWS download method Open

enhancement

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

nf-core/fetchngs#354 · Opened Aug 14, 2025
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)' Open

bug

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

nf-core/fetchngs#351 · Opened Jul 24, 2025
ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)' Open

bug

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

nf-core/fetchngs#346 · 1 comment · Opened May 12, 2025
Add support for cloud platform Open

enhancement

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

nf-core/fetchngs#345 · 1 comment · Opened May 8, 2025
Add xsra support Open

enhancement

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

nf-core/fetchngs#344 · Opened May 1, 2025
Partition error on SLURM only with fetchngs - Open

bug

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

nf-core/fetchngs#343 · Opened Apr 9, 2025
Fetchngs fails with error: terminated with an error exit status (1) -- Execution is retried (1) Open

bug

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

nf-core/fetchngs#342 · 1 comment · Opened Mar 26, 2025
fetchngs test fails Open

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

nf-core/fetchngs#336 · 2 reactions · Opened Feb 6, 2025
fasterq-dump => disk: local-ssd Open

enhancement

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

nf-core/fetchngs#332 · 3 comments · Opened Jan 11, 2025
Incorrect MD5 checksums being used for some files Open

bug

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

nf-core/fetchngs#331 · Opened Jan 9, 2025
1.11.0 works while 1.12.0 fails for apptainer+wget ( wget: unable to resolve host address 'ftp.sra.ebi.ac.uk' ) Open

bug

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

nf-core/fetchngs#328 · 3 comments · Opened Dec 9, 2024
Incorrect fastq paths in scRNA-seq sample sheet Open

bug

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

nf-core/fetchngs#326 · 1 reaction · Opened Nov 29, 2024
Update some modeles for TES compliance Open

bug

nf-core/fetchngs#318 · 1 assignee · Opened Sep 13, 2024
SRATOOLS_FASTERQDUMP failing due to missing fastq file Open

bug

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

nf-core/fetchngs#317 · 11 comments · Opened Jul 24, 2024
Support for CNBG Open

enhancement

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

nf-core/fetchngs#315 · Opened Jul 1, 2024
DDBJ study ids (DRP123456) do not map correctly Open

bug

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

nf-core/fetchngs#314 · Opened Jul 1, 2024
Support for GSA accessions Open

enhancement

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

nf-core/fetchngs#313 · 2 reactions · Opened May 30, 2024
SRA file links deprecated Open

bug

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

nf-core/fetchngs#301 · 3 comments · Opened Mar 7, 2024
wget host address error Open

bug

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

nf-core/fetchngs#291 · 13 comments · 2 reactions · Opened Feb 23, 2024
Merge technical replicates (SRR1 + SRR2 -> SRX) Open

enhancement

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

nf-core/fetchngs#270 · Opened Feb 6, 2024
Add ability to download more than 2 FastQ files via FTP and Aspera Open

enhancement

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

nf-core/fetchngs#260 · 3 comments · Opened Jan 30, 2024
check out extensions for input files Open

bug

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

nf-core/fetchngs#256 · 3 comments · Opened Jan 25, 2024
Use nf-test for input validation Open

enhancement

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

nf-core/fetchngs#254 · Opened Jan 18, 2024
FEAT: Pass scientific name as input to download the data Open

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

nf-core/fetchngs#235 · Opened Nov 2, 2023
SRAtools download seems to insert paired-end suffix into workdir path Open

bug

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

nf-core/fetchngs#221 · 7 comments · Opened Oct 16, 2023
Add compatibility with sarek samplesheet Open

enhancement

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

nf-core/fetchngs#196 · Opened Sep 21, 2023
Deal with accessions with non-existing files Open

enhancement

nf-core/fetchngs#139 · 7 comments · 1 assignee · Opened Mar 24, 2023
eutils rate limits exceeded (with relatively small input set of accessions) Open

bug

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

nf-core/fetchngs#117 · 4 comments · 1 reaction · Opened Oct 13, 2022
Use ffq to fetch id metadata Open

enhancement

nf-core/fetchngs#110 · 1 assignee · Opened Jul 21, 2022
Can SRA responses be trapped and reported in a user-friendly manner? Open

enhancement

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

nf-core/fetchngs#108 · 1 comment · Opened Jul 14, 2022
add --save_merged_fastq for merging technical repeats to fetchngs Open

enhancement

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

nf-core/fetchngs#95 · 5 comments · 1 reaction · Opened Jun 7, 2022
Allow a prepared ENA metadata samplesheet as input Open

enhancement

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

nf-core/fetchngs#77 · 1 comment · Opened Mar 7, 2022
Check if running offline Open

enhancement

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

nf-core/fetchngs#18 · 1 comment · Opened Jun 29, 2021

nf-core/fetchngs

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