epi2me-labs/wf-single-cell

Issues

• Missing output/ intermediary files

  #113 opened a month ago by lauratwomey
  3

• processes got stuck on large input

  #119 opened 15 days ago by wanghlv
  2

• the new reference release by 10x

  #118 opened 20 days ago by wanghlv
  2

• adapters and barcode/UMI trimmed reads

  #117 opened 20 days ago by wanghlv
  2

• 5prime v3

  #116 opened 21 days ago by xianliaogithub
  1

• Custom reference genes do not populate feature matrix

  #98 opened 2 months ago by Jason-Eigenbrood
  10

• OSError: [Errno 28] No space left on device

  #114 opened a month ago by lscdanson
  3

• Gene expression levels and Transcript expression levels don't correlate

  #99 opened a month ago by pratarora
  1

• Problem with symlinks in fastq input directory

  #103 opened a month ago by HenriettaHolze
  2

• Can this pipeline work with other methods besides 10x?

  #112 opened a month ago by mpage21
  1

• Recommendation for read filtering and trimming

  #107 opened a month ago by HenriettaHolze
  2

• Error while running pipeline with 10x -3 prime v4 kit

  #108 opened a month ago by Bioinfo9
  2

• cannot cache function 'rdist'

  #111 opened a month ago by davidebolo1993
  1

• Transcripts with class_code "u" in gene expression matrix

  #110 opened a month ago by kataksk
  1

• Support for 5' kit version 2?

  #106 opened 2 months ago by itslittman
  2

• Use PCR duplicates for error correction?

  #109 opened a month ago by itslittman
  1

• rerun generate cell whitelist without run the previous steps

  #79 opened 2 months ago by chenghuihui2018
  3

• Spiked hg38 ref aligns but does not report spike-in gene/transcript features

  #70 opened 6 months ago by Fractal10
  4

• Workflow fails during tag_bam, for some datasets.

  #105 opened 2 months ago by ddiez
  4

• Error in pipeline:process_bams:process_matrix

  #102 opened 2 months ago by HenriettaHolze
  6

• Error in pipeline:process_bams:tag_bam

  #100 opened 2 months ago by HenriettaHolze
  6

• Fusion Detection with wf-single-cell

  #104 opened 2 months ago by cristoforo88
  1

• samtools: unrecognized option '--no-PG'

  #96 opened 2 months ago by MaestSi
  3

• Compatible with Visium platform

  #101 opened 2 months ago by Qirongmao97
  1

• Isoform-level expression count matrix?

  #92 opened 3 months ago by sheetsvicky
  2

• use of licensed conda channels

  #93 opened 2 months ago by trum994
  1

• Problems with v2.0.0

  #97 opened 2 months ago by ddiez
  5

• Running multiplexed files

  #90 opened 2 months ago by mcortes-lopez
  1

• Error executing process > 'parse_kit_metadata (1)' with singularity

  #87 opened 2 months ago by ktpolanski
  5

• pipeline:process_bams:stringtie (23)` terminated with an error exit status (143)

  #77 opened 2 months ago by Jason-Eigenbrood
  4

• "Cannot allocate memory" during stringtie

  #72 opened 2 months ago by ktpolanski
  5

• error executing process > 'pipeline:process_bams:extract_barcodes (74) '

  #75 opened 2 months ago by reedmakGCB
  7

• Wrong strandness assumed for multiome v1?

  #78 opened 2 months ago by iaaka
  12

• Error executing process > 'pipeline:process_bams:combine_bams_and_tags (1)'

  #81 opened 2 months ago by ktpolanski
  12

• Cellranger style output count matrices - sparse, raw, full gene space

  #80 opened 2 months ago by ktpolanski
  6

• Alignment without genes.gtf

  #82 opened 2 months ago by JuanruMaryGuo
  1

• cannot open input file {sample}.stringtie.gff -- Command fails for one sample but runs for others

  #83 opened 2 months ago by pratarora
  2

• Very small output BAM file (wrong BAM file processed by tag_bams?)

  #85 opened 2 months ago by porchard
  3

• is the wf-sc workflow modular?

  #88 opened 2 months ago by Sefi196
  1

• unable to download the wf-single-cell

  #86 opened 2 months ago by yuanwsy
  4

• Issue running v1.1.0 on demo dataset

  #95 opened 2 months ago by MaestSi
  2

• Only UMAP for one sample in HTML report

  #94 opened 3 months ago by ddiez
  2

• Request for uopdate to docker with stringtie v2.2

  #91 opened 3 months ago by pratarora
  1

• Concerns with logic behind stringtie step

  #89 opened 3 months ago by kwells4
  2

• pipeline:makeReport (1)` terminated with an error exit status (1)

  #71 opened 4 months ago by cihaterdogan
  12

• GFF isoform output for follow-up SQANTI3 analysis

  #69 opened 5 months ago by Qirongmao97
  2

• Error executing process > 'pipeline:process_bams:tag_bams (14)

  #76 opened 5 months ago by Jason-Eigenbrood
  5

• Visium config

  #74 opened 5 months ago by davidebolo1993
  2

• All integer `UY` column breaks tag_bam.py

  #73 opened 5 months ago by ktpolanski
  3

• Identifying full-length transcripts / adapter configuration

  #68 opened 7 months ago by LynnLy
  2