when clusters are factor some of the celltypes are coming us as number, not getting assigned any cell type.

[nfancy]

by changing the nf-core-scflow rscript using the following did not help, rather intorduced new error as follows:

sce$clusters <- as.numeric(as.character(sce$clusters))

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'scflow_finalize (merged)'

Caused by:
  Process `scflow_finalize (merged)` terminated with an error exit status (1)

Command executed:

  scflow_finalize_sce.r       --sce_path celltype_mapped_sce       --celltype_mappings celltype_mappings.tsv       --clusters_colname clusters       --celltype_var cluster_celltype       --unique_id_var manifest       --facet_vars manifest,diagnosis,group,apoe,sex       --input_reduced_dim UMAP_Liger       --metric_vars pc_mito,pc_ribo,total_counts,total_features_by_counts

Command exit status:
  1

Command output:
  (empty)

Command error:
  �[33mWARNING:�[0m destination /rds/general/user/nfancy/ephemeral/tmp_mathys/a2/a70fd2dd5567eac3452a6b461f497d already in mount list: destination is already in the mount point list
  Warning message:
  replacing previous import ‘liger::normalize’ by ‘scater::normalize’ when loading ‘scFlow’ 
  
  ── Reading Celltype Mappings ───────────────────────────────────────────────────
  Reading: celltype_mappings.tsv
  ✔ Imported celltype mappings from celltype_mappings.tsv
  
  ── Reading SingleCellExperiment ────────────────────────────────────────────────
  
  ── Reading feature-barcode matrix ──
  
  Reading: celltype_mapped_sce/barcodes.tsv.gz
  Reading: celltype_mapped_sce/features.tsv.gz
  Reading: celltype_mapped_sce/matrix.mtx.gz
  ✔ Imported sparse matrix: 53273 cols x 17048 rows.
  
  ── Reading colData/rowData ──
  
  Reading: celltype_mapped_sce/sce-rowdata.tsv
  Reading: celltype_mapped_sce/scecoldata_classes.tsv
  Reading: celltype_mapped_sce/sce-coldata.tsv
  Generating SingleCellExperiment
  Reading: ReducedDim_Liger.tsv
  Reading: ReducedDim_PCA_PB.tsv
  Reading: ReducedDim_PCA.tsv
  Reading: ReducedDim_tSNE_Liger.tsv
  Reading: ReducedDim_tSNE_PCA.tsv
  Reading: ReducedDim_UMAP_Liger.tsv
  Reading: ReducedDim_UMAP_PCA_PB.tsv
  Reading: ReducedDim_UMAP_PCA.tsv
  Reading: ReducedDim_UMAP3D_Liger.tsv
  Reading: ReducedDim_UMAP3D_PCA.tsv
  ✔ Imported SingleCellExperiment.
  Appended `Allan2019_ML1` to SingleCellExperiment
  Appended `Allan2019_ML2` to SingleCellExperiment
  Appended `Zeisel2018_ML4` to SingleCellExperiment
  Appended `Zeisel2018_ML5` to SingleCellExperiment
  Appended `allan_celltype` to SingleCellExperiment
  Appended `allan_layer` to SingleCellExperiment
  Appended `allan_cluster_gene_1` to SingleCellExperiment
  Appended `allan_cluster_gene_2` to SingleCellExperiment
  Appended `cluster_celltype` to SingleCellExperiment
  Error: Specify categorical variables only.
  Execution halted

Work dir:
  /rds/general/user/nfancy/ephemeral/tmp_mathys/a2/a70fd2dd5567eac3452a6b461f497d

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[combiz]

resolved by 73ca596