issues Search Results · repo:nf-core/fetchngs language:Nextflow
Filter by
88 results
(80 ms)88 results
innf-core/fetchngs (press backspace or delete to remove)Description of the bug
I am trying to download metadata associated with a bunch of SRR ids and the fetchngs flow is failing. The code I am
using is nextflow run nf-core/fetchngs
-c samples_fetchngs_20250319.config ...
bug
kanekalla
- Opened 3 days ago
- #342
Description of feature
Hi and thanks for providing this nice pipeline it really saves me a lot of time and headache when downloading large
amounts of published data. However, recently I found some hiccups ...
enhancement
dmalzl
- Opened 10 days ago
- #340
I trying the fetchngs pipeline but I can t even get the test to run. Any advice? see log below.
best, sb
nextflow run nf-core/fetchngs -profile test,singularity --outdir test -resume
Nextflow 24.10.4 ...
mjfi2sb3
- Opened on Feb 6
- #336
Description of feature
As far as I can tell, the fasterqdump module does not set disk.
Setting the disk to local-ssd for use with google-batch could be quite helpful for speeding up the writing of temp ...
enhancement
nick-youngblut
- 3
- Opened on Jan 11
- #332
Description of the bug
I ve been having an issue with some files failing at checksum in some studies. Upon investigation, for at least some of
these failing samples, it appears to be due to the pipeline ...
bug
tanaes
- Opened on Jan 9
- #331
Description of the bug
Hi all,
the workflow works with 1.11.0
$ cat ids.csv
ERR861313
rm -rf work module load apptainer nextflow run nf-core/fetchngs -r 1.11.0 -profile apptainer,glicid -resume ...
bug
lindenb
- 1
- Opened on Dec 9, 2024
- #328
Description of the bug
I am trying to use fetchngs to download scRNA-seq data from
[SRP348981](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA785648 o=acc_s%3Aa s=SRR17102627,SRR17102614) and
prepare ...
bug
huldash
- Opened on Nov 29, 2024
- #326
Description of the bug
Two modules need updates to be tes compliance
- multiqc_mappings_config
- sratools/prefetch
Command used and terminal output
No response
Relevant files
No response
System ...
bug
vsmalladi
- Opened on Sep 13, 2024
- #318
Description of the bug
I have a list of SRR IDs in a file and am trying to download them using the pipeline. However, I constantly get an error
at the SRATOOLS_FASTERQDUMP step.
This is an example of ...
bug
edg1983
- 11
- Opened on Jul 24, 2024
- #317
Description of feature
Recently a lot of interesting data has been landing in CNBGdb (https://db.cngb.org/)
Is there any plan to implement support for this database? Is this something I as a novice could ...
enhancement
nathaniel-mahieu
- Opened on Jul 1, 2024
- #315
Learn how you can use GitHub Issues to plan and track your work.
Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub IssuesProTip!
Press the /
key to activate the search input again and adjust your query.Learn how you can use GitHub Issues to plan and track your work.
Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub IssuesProTip!
Restrict your search to the title by using the in:title qualifier.