epi2me-labs wf-single-cell issues

epi2me-labs / wf-single-cell

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All cells filtered out when using bam as input

#146 Josephinedh opened 4 days ago
0
ERROR ~ Error executing process > 'pipeline:process_bams:process_matrix (1)'

#145 zhujack opened 3 weeks ago
4
Python/minimap2 not found when running v2.3.0 using Singularity on demo data

#144 gabyrech opened 3 weeks ago
5
Error due to number deprecation

#143 Coracollar closed 1 month ago
5
umi_gene_saturation error 137

#142 lizh0205 opened 1 month ago
5
TSO artefacts

#141 remiolsen closed 1 month ago
2
Only unknown transcripts

#140 HenriettaHolze closed 1 month ago
6
Recover unmapped reads

#139 HenriettaHolze closed 2 months ago
1
Visium v1 Spatial analysis

#138 MustafaElshani closed 1 month ago
3
Requesting detailed information about each read

#137 sagnikbanerjee15 closed 1 month ago
2
Questions about the Barcode/UMI correction

#136 Francais0620 opened 3 months ago
2
How is collapsing of the corrected UMIs for transcript quantification done?

#135 skudashev closed 3 months ago
2
Return the unfiltered matrix

#134 ddiez opened 3 months ago
9
GEM-X compatibility

#133 ECRWatson closed 2 months ago
2
How to use custom parameters for barcode and UMI length?

#132 MenglinC closed 3 months ago
5
wf-single-cell HTML report shows incorrect number of the Input reads

#131 jackchenx3 closed 3 months ago
2
Failed to pull singularity image | status : 255

#130 MenglinC closed 3 months ago
1
Failed to pull singularity image | status : 255

#129 Francais0620 closed 3 months ago
2
I can't find a summary file for the pipeline

#128 jackchenx3 closed 3 months ago
2
Reads without adaptor/primer won't be used, so duplex reads will not be used in wf-single-cell?

#127 ErminZ closed 1 month ago
4
Combining short and long reads with StringTie --mix

#126 Jason-Eigenbrood closed 1 month ago
1
`pipeline:process_bams:stringtie (1)` terminated with an error exit status (1)

#125 sme229 closed 1 month ago
8
NUMBA RuntimeError related to cachedir

#124 CloXD closed 4 months ago
2
ValueError: The expression matrix contains no cells

#123 sme229 closed 4 months ago
3
support 3primeV4 chemistry

#122 yinshiyi closed 4 months ago
1
RuntimeError: cannot cache function 'rdist': no locator available

#121 sme229 closed 4 months ago
2
3prime v4 support

#120 Lisa-We closed 2 months ago
2
processes got stuck on large input

#119 wanghlv closed 4 months ago
4
the new reference release by 10x

#118 wanghlv closed 4 months ago
2
adapters and barcode/UMI trimmed reads

#117 wanghlv closed 4 months ago
2
5prime v3

#116 xianliaogithub opened 4 months ago
4
Time directives for all processes

#115 WardDeb closed 5 months ago
2
OSError: [Errno 28] No space left on device

#114 lscdanson closed 2 months ago
7
Missing output/ intermediary files

#113 lauratwomey closed 2 months ago
5
Can this pipeline work with other methods besides 10x?

#112 mpage21 closed 5 months ago
1
cannot cache function 'rdist'

#111 davidebolo1993 closed 5 months ago
1
Transcripts with class_code "u" in gene expression matrix

#110 kataksk closed 2 months ago
2
Use PCR duplicates for error correction?

#109 itslittman closed 4 months ago
3
Error while running pipeline with 10x -3 prime v4 kit

#108 Bioinfo9 closed 5 months ago
2
Recommendation for read filtering and trimming

#107 HenriettaHolze closed 5 months ago
2
Support for 5' kit version 2?

#106 itslittman closed 5 months ago
2
Workflow fails during tag_bam, for some datasets.

#105 ddiez closed 6 months ago
4
Fusion Detection with wf-single-cell

#104 cristoforo88 closed 6 months ago
1
Problem with symlinks in fastq input directory

#103 HenriettaHolze closed 5 months ago
2
Error in pipeline:process_bams:process_matrix

#102 HenriettaHolze closed 6 months ago
6
Compatible with Visium platform

#101 Qirongmao97 closed 6 months ago
1
Error in pipeline:process_bams:tag_bam

#100 HenriettaHolze closed 6 months ago
6
Gene expression levels and Transcript expression levels don't correlate

#99 pratarora closed 5 months ago
1
Custom reference genes do not populate feature matrix

#98 Jason-Eigenbrood closed 4 months ago
13
Problems with v2.0.0

#97 ddiez closed 6 months ago
5