nf-core/rnasplice

Issues

• Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SRX12134688)', Caused by: Process `NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SRX12134688)` terminated with an error exit status (255)

  #151 opened 4 months ago by tud03125
  32

• Miso ERROR

  #150 opened 4 months ago by torres-HI
  12

• Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:CREATE_BAMLIST_SINGLE (1)' caused by: No such variable: bam -- Check script '/home/tud03125/.nextflow/assets/nf-core/rnasplice/./workflows/../subworkflows/local/../../modules/local/create_bamlist_single.nf' at line: 20

  #152 opened 4 months ago by tud03125
  1

• AWSmegatests are failing

  #144 opened 7 months ago by FriederikeHanssen
  5

• Miso error

  #134 opened 8 months ago by BulutHamali
  10

• Implement IsoformSwitchAnalyzeR

  #148 opened 5 months ago by jesseangelis
  2

• Spare memory for samtools issue

  #145 opened 7 months ago by bc2zb
  1

• DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names

  #140 opened 7 months ago by fhausmann
  0

• Merged genes output

  #139 opened 7 months ago by SergioManzano10
  3

• ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'

  #126 opened 10 months ago by IanCodes
  11

• RNA splice output

  #138 opened 8 months ago by SergioManzano10
  0

• `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)`

  #137 opened 8 months ago by SergioManzano10
  7

• Error in SUPPA: Clustergroups are assigned incorrectly

  #131 opened 8 months ago by spraeger
  4

• sashimi_plot error

  #111 opened a year ago by GimenaA
  2

• Error in DRIMSeq::dmDSdata(counts = counts, samples = samps)

  #129 opened 9 months ago by GimenaA
  3

• Error single-end execution

  #130 opened 9 months ago by fcastillo1
  1

• MISO error

  #119 opened 9 months ago by ZeinBader
  3

• Error: suppa_split_file.R Input_file must contain samplesheet samples.

  #122 opened a year ago by Mridul-Chaudhary
  2

• The processes for splitting files are running very slowly with large numbers of input samples

  #120 opened a year ago by amizeranschi
  5

• EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a

  #117 opened a year ago by petemeng
  2

• Empty output for BAM+rMats

  #105 opened a year ago by Qingru44004
  2

• link to example contrastsheet.csv is not working

  #104 opened a year ago by Jokendo-collab
  1

• DEXSeq-DTU Stager pScreenAdjusted

  #108 opened a year ago by bio-info-guy
  1

• contrast file problem?

  #112 opened a year ago by marwa38
  7

• Missing rMATS arguments

  #107 opened a year ago by adomingues
  2

• STAGER error: subscript out of bounds

  #99 opened a year ago by paolo-kunderfranco
  4

• make contrasts file names consistent with those of the differentialabundance pipeline

  #106 opened a year ago by adomingues
  1

• DRIMSEQ_FILTER error

  #98 opened a year ago by DwinGrashof
  5

• Add some more tags to make the pipeline easier to find

  #97 opened a year ago by FriederikeHanssen
  1

• STAGER error: subscript out of bounds

  #83 opened a year ago by paolo-kunderfranco
  6

• example contrastsheet.csv missing

  #93 opened a year ago by Kevin2197
  1

• MISO_SASHIMI error: Could not find MISO output files

  #89 opened a year ago by amizeranschi
  4

• test profile: miso_index failure

  #90 opened a year ago by heathfuqua
  19

• SUPPA cluster events error

  #71 opened a year ago by paolo-kunderfranco
  14

• The pipeline should be able to infer strandedness from FASTQ (i.e. allow "auto" for strandedness in the CSV)

  #84 opened a year ago by amizeranschi
  2

• Error with rmats.py when running with multiple contrasts: <filename>.bam not found in .rmats files

  #85 opened a year ago by amizeranschi
  10

• The default --miso_genes are invalid when --gencode is specified and cause the pipeline to fail

  #78 opened a year ago by amizeranschi
  2

• DRIMSEQ_FILTER error

  #69 opened a year ago by paolo-kunderfranco
  10

• GTF_2_GFF3 fails with latest Gencode GTF for human

  #72 opened a year ago by amizeranschi
  21

• EDGER_EXON fails if only single entry in contrast sheet

  #81 opened a year ago by dkoppstein
  1

• MISO_SASHIMI looks in NXF_HOME subdirectory instead of working directory for output files

  #75 opened a year ago by dkoppstein
  4

• MISO_SASHIMI step fails when using scratch directory

  #74 opened a year ago by dkoppstein
  2

• ERROR ~ No such variable: Exception evaluating property 'out' for nextflow.script.ChannelOut

  #70 opened a year ago by amizeranschi
  7

• dexseq: stager.R: subscript out of bounds.

  #44 opened 2 years ago by gl9797
  2

• check_contrastsheet not identifying headers even though they're present

  #63 opened 2 years ago by expansion-bioemformatics
  2

• prepare_genome gencode

  #60 opened 2 years ago by tijeco
  2