nf-core rnaseq issues - Githubissues

nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

https://nf-co.re/rnaseq

MIT License

921 stars 708 forks source link

issues

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Inconsistent sequence and quality lengths in FASTQ files created by SortMeRNA

#1456 cihanerkut opened 19 hours ago
0
singularity.registry ignored when pulling nf-core/bedtools_coreutils image

#1455 mathob opened 1 day ago
4
The pipeline skips most steps when the sortmerna index is provided

#1454 davidecarlson opened 1 day ago
1
Initial commit to add fq lint module

#1453 oligomyeggo opened 1 week ago
0
The parameter "save_trimmed=true" mistakenly activates merging mode of fastp

#1452 yxkwgp opened 1 week ago
0
ERROR: stage minimap2_transcriptome failed: Command in stage minimap2_transcriptome failed with exit status = 127

#1451 KRothamel opened 1 week ago
0
Warn user if both `transcript_fasta` and `additional_fasta` are provided.

#1450 siddharthab opened 1 week ago
0
Sample name changed 3.16

#1449 fjosefdz opened 2 weeks ago
0
osx arm64/v8 failure on profile test,docker

#1448 PikalaxALT opened 2 weeks ago
0
Adding differential expression analysis tutorial pages to Usage section

#1447 LorenzoS96 closed 1 week ago
0
Pipeline prefixes X to samplenames

#1446 RaverJay opened 3 weeks ago
0
Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries

#1445 RaverJay opened 3 weeks ago
2
root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system

#1444 JinchaoChen112 opened 3 weeks ago
0
transfer nf-core/rnaseq tutorial on nf-core/rnaseq repo

#1443 lescai closed 3 weeks ago
1
RSeQC module tin.py creates RefseqID instead of ENSEMBLIDs of transcripts

#1442 AnissaE opened 3 weeks ago
0
Fix nf-core download test

#1441 maxulysse closed 4 weeks ago
5
Reduce matrix

#1440 maxulysse closed 4 weeks ago
1
Try matthias' fix to download

#1439 pinin4fjords opened 4 weeks ago
2
implement sharding of tests

#1438 maxulysse opened 4 weeks ago
1
update CHANGELOG

#1437 maxulysse closed 4 weeks ago
0
[do not merge] remove isMaster block to see how it affects the matrix (master)

#1436 adamrtalbot closed 4 weeks ago
2
[do not merge] remove isMaster block to see how it affects the matrix (dev)

#1435 adamrtalbot closed 4 weeks ago
1
No exception for default registry

#1434 maxulysse closed 4 weeks ago
1
Dev -> Master for 3.17.0

#1433 pinin4fjords closed 4 weeks ago
1
Bump versions for 3.17.0 release

#1432 pinin4fjords closed 4 weeks ago
2
Remove need for use of Seqera conda channels

#1431 pinin4fjords opened 4 weeks ago
0
Add ARM support for hisat2

#1430 pinin4fjords opened 4 weeks ago
0
Add ARM support for Bracken

#1429 pinin4fjords opened 4 weeks ago
0
Add ARM support for kraken2

#1428 pinin4fjords opened 4 weeks ago
0
Revision of the code of RNAseq tutorial

#1427 LorenzoS96 closed 3 weeks ago
0
Revision of Theory paragraphs of RNAseq tutorial

#1426 LorenzoS96 closed 3 weeks ago
0
Add profile for ARM compatibility

#1425 pinin4fjords closed 4 weeks ago
3
patch sortmerna to 4.3.7 for ARM compatibility

#1424 pinin4fjords closed 1 month ago
2
Bump STAR version for version with ARM Conda build

#1423 pinin4fjords closed 1 month ago
1
Bump lots of modules so that conda versions have arm builds

#1422 pinin4fjords closed 1 month ago
2
allow integer sample names

#1421 idot opened 1 month ago
2
strandness error

#1420 aheravi opened 1 month ago
2
3.16.x does not allow numeric sample ids

#1419 idot opened 1 month ago
2
Bump versions back to 3.17.0 after release

#1418 pinin4fjords closed 1 month ago
1
Update dev from master

#1417 pinin4fjords closed 1 month ago
2
Properly disable conda pipeline level tests

#1416 maxulysse closed 1 month ago
1
FIX: Disable pipeline level conda tests

#1415 maxulysse closed 1 month ago
1
Backport support for Graviton 4 to version 3.16.1

#1414 pabloaledo closed 1 month ago
4
Dev -> Master for 3.16.1

#1413 pinin4fjords closed 1 month ago
1
Reset versions back to 3.16.1 for patch release

#1412 pinin4fjords closed 1 month ago
1
Backport support for Graviton 4 to upstream rnaseq

#1411 pditommaso closed 1 month ago
2
Fix issues caused by empty versions from trimming subworkflows

#1410 pinin4fjords closed 1 month ago
1
Fix manifest text

#1409 maxulysse closed 1 month ago
2
bbsplit behavior with ambiguous reads : --extra_bbsplit_args possible to add ?

#1408 ZheFrench closed 1 month ago
3
Important! Template update for nf-core/tools v3.0.2

#1407 nf-core-bot closed 1 month ago
2