vib-singlecell-nf/vsn-pipelines

Issues

• [BUG] Cannot invoke method containsKey() on null object

  #382 opened 3 years ago by AlinaKurjan
  2

• throw new Exception("Cannot append SCENIC loom to SCope loom because the IDs do not match.")[BUG]

  #392 opened 2 years ago by LinearParadox
  6

• [BUG] Cannot invoke method containsKey() on null object

  #378 opened 3 years ago by HocheolJang426
  2

• ARBORETO_WITH_MULTIPROCESSING fails to start

  #388 opened 2 years ago by GreyRockIQ
  0

• single-sample_test error

  #385 opened 3 years ago by GreyRockIQ
  0

• pipeline executing error

  #387 opened 3 years ago by GreyRockIQ
  0

• FATAL: container creation failed: mount

  #373 opened 3 years ago by gianfilippo
  2

• [BUG] Unknown configuration profile: 'single_sample_decontx_scrublet'

  #381 opened 3 years ago by s-aibar
  0

• docker error unknown shorthand flag: 'B' in -B while running the pipeline

  #377 opened 3 years ago by MarcDalod
  1

• [BUG] There is no package called "SeuratObject"

  #376 opened 3 years ago by alefrol638
  0

• [BUG] scenic multirun stalls during Arboreto with multiprocessing

  #375 opened 3 years ago by Jay-Leung
  0

• [BUG] Include statement is not allowed within a workflow definition

  #369 opened 3 years ago by matt-sd-watson
  9

• Include statement is not allowed within a workflow definition

  #372 opened 3 years ago by gianfilippo
  2

• [SUGGESTION] Add Median genes/UMIs to Reporting

  #367 opened 3 years ago by KrisDavie
  0

• [SUGGESTION] Include a check for config version

  #315 opened 3 years ago by KrisDavie
  1

• [SUGGESTION] Update scanpy

  #316 opened 3 years ago by cflerin
  3

• Error starting from h5ad [BUG]

  #300 opened 3 years ago by cbravo93
  3

• [SUGGESTION] Handle both verisons of HyDrop ATAC

  #352 opened 3 years ago by cflerin
  0

• [NEW TOOL] fastp (adapter trimming)

  #326 opened 3 years ago by cflerin
  0

• [SUGGESTION] Migrating config from params.sc.<tool>.* to params.tools.<tool>.*

  #310 opened 3 years ago by dweemx
  0

• [BUG] SRA workflow not working for scATAC-seq samples

  #348 opened 3 years ago by dweemx
  0

• Using flavor='seurat_v3' for feature selection may give better results [SUGGESTION]

  #354 opened 3 years ago by cbravo93
  2

• SC__SCANPY__DIM_REDUCTION: nComps is both statically and dynamically[BUG]

  #365 opened 3 years ago by Zifeng-L
  2

• Failed to find loop device[BUG]

  #364 opened 3 years ago by Zifeng-L
  0

• [BUG] Error: Cannot append SCENIC loom to SCope loom because the IDs do not match

  #363 opened 3 years ago by iUser1234
  0

• [BUG] Failing to parse SRA metadata

  #360 opened 3 years ago by dweemx
  0

• [BUG] loomHandler.nf - process PUBLISH_LOOM record container is missing

  #359 opened 3 years ago by Hynst
  0

• Scrublet: ValueError: columns overlap but no suffix specified: Index(['nGene', 'nUMI'], dtype='object') [BUG]

  #353 opened 3 years ago by cbravo93
  1

• [SUGGESTION] Take 10x Multiome data as inputs

  #351 opened 3 years ago by cflerin
  0

• [singlecelltoolkit] [SUGGESTION] Add script to calculate saturation curve of 10x samples

  #332 opened 4 years ago by dweemx
  2

• [SUGGESTION] Input of MEX files from non-cellranger formats

  #350 opened 4 years ago by cflerin
  0

• single_sample_scrublet with different resolution parameters returns a loom file with only clustering for the last resolution listed[BUG]

  #303 opened 4 years ago by cbravo93
  0

• [BUG] output without suffix, and no loom published

  #345 opened 4 years ago by atomnh
  1

• [BUG] the Nextflow version reported in the docs is likely wrong

  #329 opened 4 years ago by lucacozzuto
  1

• [BUG]

  #343 opened 4 years ago by atomnh
  0

• [SUGGESTION] [harmony] Allow to specify multiple batch variables

  #292 opened 4 years ago by dweemx
  0

• [SUGGESTION] Allow to tag group of files

  #291 opened 4 years ago by dweemx
  0

• [BUG] Cannot run VSN without job submission system

  #321 opened 4 years ago by Ijoanito
  4

• [BUG] compute resources labels not correctly applied to some processes

  #323 opened 4 years ago by cflerin
  1

• [SUGGESTION] Add zlib-ng for speedup of gzip/zlib (de)compression

  #325 opened 4 years ago by dweemx
  1

• Error when providing loom with metadata as input (single_sample_scrublet) [BUG]

  #301 opened 4 years ago by cbravo93
  0

• Scrublet metadata in loom is nan [BUG]

  #302 opened 4 years ago by cbravo93
  4

• failed to create hard link ‘pbmc10k_data.SCANPY.hvg_scaled_output.h5ad’ => ‘tmp’: Operation not permitted

  #317 opened 4 years ago by vagabond12
  7

• [SUGGESTION] Add a quiet mode

  #283 opened 4 years ago by cflerin
  0

• [BUG] normalize_per_cell can lead to not exact reproducible results with mixed data

  #295 opened 4 years ago by dweemx
  0

• [SUGGESTION] Add uncorrected UMAP/tSNE when using batch effect correction (e.g. Harmony/BBKNN)

  #337 opened 4 years ago by cbravo93
  0

• [NEW TOOL] Add ATAC-DoubletDetector

  #333 opened 4 years ago by dweemx
  0

• [BUG] [scenic] Regulons can be missing in multi-runs mode

  #319 opened 4 years ago by dweemx
  0

• [SUGGESTION] Avoid correction of barcode names

  #288 opened 4 years ago by cbravo93
  6

• [BUG] Pipeline crashing when starting from SCopeLoomR loom files

  #286 opened 4 years ago by cbravo93
  1