nf-core/rnaseq

Issues

• The parameter "save_trimmed=true" mistakenly activates merging mode of fastp

  #1452 opened a month ago by yxkwgp
  0

• ERROR: stage minimap2_transcriptome failed: Command in stage minimap2_transcriptome failed with exit status = 127

  #1451 opened a month ago by KRothamel
  0

• Warn user if both `transcript_fasta` and `additional_fasta` are provided.

  #1450 opened a month ago by siddharthab
  0

• Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries

  #1445 opened 2 months ago by RaverJay
  2

• Sample name changed 3.16

  #1449 opened 2 months ago by fjosefdz
  0

• osx arm64/v8 failure on profile test,docker

  #1448 opened 2 months ago by PikalaxALT
  0

• transfer nf-core/rnaseq tutorial on nf-core/rnaseq repo

  #1443 opened 2 months ago by lescai
  1

• Revision of Theory paragraphs of RNAseq tutorial

  #1426 opened 2 months ago by LorenzoS96
  0

• Pipeline prefixes X to samplenames

  #1446 opened 2 months ago by RaverJay
  0

• Revision of the code of RNAseq tutorial

  #1427 opened 2 months ago by LorenzoS96
  0

• root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace not supported by your system

  #1444 opened 2 months ago by JinchaoChen112
  0

• RSeQC module tin.py creates RefseqID instead of ENSEMBLIDs of transcripts

  #1442 opened 2 months ago by AnissaE
  0

• Remove need for use of Seqera conda channels

  #1431 opened 2 months ago by pinin4fjords
  0

• Add ARM support for hisat2

  #1430 opened 2 months ago by pinin4fjords
  0

• Add ARM support for Bracken

  #1429 opened 2 months ago by pinin4fjords
  0

• Add ARM support for kraken2

  #1428 opened 2 months ago by pinin4fjords
  0

• pipeline no longer compatible with newest STAR 2.7.11b

  #1316 opened 2 months ago by gvogler
  1

• 3.16.x does not allow numeric sample ids

  #1419 opened 2 months ago by idot
  2

• strandness error

  #1420 opened 2 months ago by aheravi
  2

• Helpful error message when strandedness cannot be infered

  #1390 opened 2 months ago by simoxb
  5

• External Argument Documentation

  #1313 opened 2 months ago by charlesdavid
  4

• Error running process `NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION`

  #1315 opened 6 months ago by charlesdavid
  1

• To use STAR module, how should the GTF file look like

  #1347 opened 5 months ago by huma1995
  1

• Hyphenated sample names causes downstream error

  #1364 opened 2 months ago by mniederhuber
  2

• NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SRR15731653)` terminated with an error exit status (1)

  #1348 opened 2 months ago by Dokmen
  2

• null path java error with all qc preprocessing skipping options enabled with revision 3.15.0

  #1387 opened 2 months ago by jos4uke
  1

• bbsplit behavior with ambiguous reads : --extra_bbsplit_args possible to add ?

  #1408 opened 2 months ago by ZheFrench
  3

• samtools version error message

  #1392 opened 2 months ago by sci-kai
  1

• java.nio.file.FileSystemException No space left on device

  #1400 opened 2 months ago by fjosefdz
  3

• RNAseq-3.14.0 Pipeline fails with aligner `star_rsem`

  #1375 opened 2 months ago by GerardTromp
  5

• Restore the set -C when the concerned modules are fixed

  #1404 opened 2 months ago by maxulysse
  0

• Bedtool image

  #1391 opened 3 months ago by aheravi
  4

• --extra_star_align_args

  #1378 opened 3 months ago by mtinti
  3

• Pipeline fails if sample names have hyphens

  #1377 opened 3 months ago by pinin4fjords
  0

• Option to keep chimeric reads after UMI deduplication

  #1373 opened 4 months ago by siddharthab
  1

• Stubs all the way down

  #1338 opened 6 months ago by maxulysse
  1

• Updating picard to 3.2.0 fails pipeline level tests

  #1346 opened 5 months ago by maxulysse
  2

• Improve qualimap execution time

  #1356 opened 4 months ago by PramodRaoB
  2

• Possible redundant rowname assignment in tximport.r

  #1365 opened 4 months ago by pmoris
  2

• Test profiles broken for Platform

  #1344 opened 4 months ago by pinin4fjords
  0

• SortMeRNA database version

  #1354 opened 4 months ago by wzheng0520
  3

• Unable to go from FASTQ to Salmon Quantification

  #1333 opened 4 months ago by SuhasSrinivasan
  1

• Sanity-check the sample names before committing to any data processing

  #1349 opened 5 months ago by fruce-ki
  0

• Custom content plots missing in MultiQC ouptut

  #1332 opened 5 months ago by pinin4fjords
  1

• Accept uncompressed files, for instance fastq

  #1343 opened 5 months ago by TheWizier
  1

• Add support to use the pipeline with NGS generated using zymo research kit

  #1337 opened 6 months ago by Ahmedalaraby20
  3

• NFCORE_RNASEQ takes values from global scope

  #1339 opened 6 months ago by adamrtalbot
  0

• modules missing stub

  #1327 opened 6 months ago by maxulysse
  0

• Show Salmon-based strand inference in MultiQC report

  #1318 opened 6 months ago by pinin4fjords
  1

• Add `tximport` for RSEM outputs

  #1320 opened 6 months ago by olgabot
  0