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61 Open 662 Closed
61 Open 662 Closed
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Issues list

getTrimGaloreReadsAfterFiltering function fails to extract filtered read count from TrimGalore log bug Something isn't working
#1557 opened May 30, 2025 by iraiosub
.command.run permission denied in 3.16.1, 3.17.0, 3.18.0 bug Something isn't working
#1554 opened May 13, 2025 by givtrah 3.19.0
20
Is there an way to retrieve a list of download link for all singularity images required, by which I can manually download these images easier. enhancement
#1532 opened Mar 27, 2025 by meng-hhh
Update to MultiQC 1.27.1 bug Something isn't working
#1527 opened Mar 26, 2025 by c-mertes 3.19.0
Salmon quantification output is missing genes when using gff3 annotation bug Something isn't working
#1524 opened Mar 24, 2025 by RaverJay
1
"Local" nf-core modules without singularity container builds cause issues
#1516 opened Mar 18, 2025 by pontus 3.19.0
7
Improvements for processing prokaryotic datasets using the nf-core/rnaseq pipeline enhancement
#1512 opened Mar 12, 2025 by sebschulz1
@pcolaianni @Juassis
@apalleja @sebschulz1 @txellext
4
Update StringTie to latest version enhancement
#1506 opened Feb 14, 2025 by rrdavis77
3
Issue in RNA seq pipeline bug Something isn't working
#1504 opened Feb 12, 2025 by Varda06
1
salmon seems to remove transcripts
#1500 opened Jan 31, 2025 by jedi-bogate
Execution time of module tin.py
#1498 opened Jan 29, 2025 by reshu23
ERROR Not able to pull image of ('biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0') bug Something isn't working
#1457 opened Nov 26, 2024 by ilariarossoni
singularity.registry ignored when pulling nf-core/bedtools_coreutils image bug Something isn't working
#1455 opened Nov 21, 2024 by mathob
4
Warn user if both transcript_fasta and additional_fasta are provided. enhancement
#1450 opened Nov 13, 2024 by siddharthab
Sample name changed 3.16 bug Something isn't working
#1449 opened Nov 4, 2024 by fjosefdz
Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries bug Something isn't working
#1445 opened Oct 29, 2024 by RaverJay
2
root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system bug Something isn't working
#1444 opened Oct 29, 2024 by JinchaoChen112
Remove need for use of Seqera conda channels enhancement
#1431 opened Oct 23, 2024 by pinin4fjords
@pabloaledo
Add ARM support for hisat2 enhancement wontfix This will not be worked on
#1430 opened Oct 23, 2024 by pinin4fjords
2
Add ARM support for Bracken enhancement
#1429 opened Oct 23, 2024 by pinin4fjords
@pabloaledo
2
Add ARM support for kraken2 enhancement
#1428 opened Oct 23, 2024 by pinin4fjords
@pabloaledo
2
strandness error bug Something isn't working
#1420 opened Oct 17, 2024 by aheravi
3
3.16.x does not allow numeric sample ids bug Something isn't working
#1419 opened Oct 17, 2024 by idot
3
Restore the set -C when the concerned modules are fixed
#1404 opened Oct 10, 2024 by maxulysse
Improve qualimap execution time enhancement
#1356 opened Aug 20, 2024 by PramodRaoB
3
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