Unused argument and Packages have functions with the same names errors

[MEFarhadieh]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/scflow pipeline documentation

Description of the bug

Dear Dr. Khozoie, thanks for your previous help. I used Docker and it worked. However now, there are errors in the packages have functions with the same names, and unused argument. I also tried test dataset on other systems and on my desktop in scflow-docker container, but all of them returned same errors. Additionally, I wanted explore nfcore/scflow container, but it seems It hasn't released yet at docker hub.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/scflow -profile test -r dev ,docker
2. See error:

executor >  local (17)
[56/fc7bc4] process > SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS) [100%] 1 of 1 ✔
[73/f77f90] process > SCFLOW:SCFLOW_QC (finov)                       [100%] 6 of 6 ✔
[4b/0a8107] process > SCFLOW:SCFLOW_MERGEQCTABLES (MERGEQCTABLES)    [100%] 1 of 1 ✔
[27/69b5a5] process > SCFLOW:SCFLOW_MERGE (MERGED)                   [100%] 1 of 1 ✔
[72/58ad73] process > SCFLOW:SCFLOW_INTEGRATE (MERGED)               [100%] 1 of 1 ✔
[f9/69935e] process > SCFLOW:SCFLOW_REDUCEDIMS (MERGED)              [100%] 1 of 1 ✔
[91/8201fb] process > SCFLOW:SCFLOW_CLUSTER (MERGED)                 [100%] 1 of 1 ✔
[66/5a4db6] process > SCFLOW:SCFLOW_REPORTINTEGRATED (MERGED)        [100%] 1 of 1 ✔
[e5/f33209] process > SCFLOW:SCFLOW_MAPCELLTYPES (MERGED)            [100%] 1 of 1 ✔
[ee/448b5d] process > SCFLOW:SCFLOW_FINALIZE (MERGED)                [100%] 1 of 1, failed: 1 ✘
[-        ] process > SCFLOW:SCFLOW_DGE                              -
[-        ] process > SCFLOW:SCFLOW_IPA                              -
[-        ] process > SCFLOW:SCFLOW_DIRICHLET                        -
[56/0db475] process > SCFLOW:SCFLOW_PLOTREDDIMGENES (MERGED)         [100%] 1 of 1 ✔
[3e/d1f397] process > SCFLOW:GET_SOFTWARE_VERSIONS (Version Info)    [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/scflow] Pipeline completed with errors-
Error executing process > 'SCFLOW:SCFLOW_FINALIZE (MERGED)'

Caused by:
  Process `SCFLOW:SCFLOW_FINALIZE (MERGED)` terminated with an error exit status (1)

Command executed:

  export MC_CORES=2
  
  scflow_finalize_sce.r     --clusters_colname clusters     --celltype_var cluster_celltype     --unique_id_var manifest     --facet_vars manifest,diagnosis,sex     --input_reduced_dim UMAP_Liger     --metric_vars pc_mito,pc_ribo,total_counts,total_features_by_counts     --top_n 5     --reddimplot_pointsize 1     --reddimplot_alpha 0.8     --sce_path celltype_mapped_sce     --celltype_mappings celltype_mappings.tsv
  
  scflow_version=$(Rscript -e 'cat(as.character(utils::packageVersion("scFlow")))'); echo "scFlow ${scflow_version}" > "scFlow_${scflow_version}.version.txt"

Command exit status:
  1

Command output:
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Command error:
  Attaching package: ‘DelayedArray’
  
  The following objects are masked from ‘package:matrixStats’:
  
      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  
  The following objects are masked from ‘package:base’:
  
      aperm, apply, rowsum
  
  
  ── 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: 1332 cols x 3484 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.
  
  ── Finding Top Marker Genes ────────────────────────────────────────────────────
  → Finding markers for cells grouped by `cluster_celltype`
  → Finding markers for cells grouped by `clusters`
  Error in (function (sce, feature_dim = "Cluster", reduced_dim = "UMAP",  : 
    unused argument (top_n = 5)
  Calls: annotate_celltype_metrics -> do.call
  In addition: Warning messages:
  1: In if (axis_order == "marker_group") { :
    the condition has length > 1 and only the first element will be used
  2: In if (axis_order == "marker_group") { :
    the condition has length > 1 and only the first element will be used
  Execution halted

System

• Hardware: Cloud
• Executor: local
• OS: Ubuntu Linux
• Version: 20.04

Nextflow Installation

• Version: 22.04.0

Container engine

• Engine: Docker
• version: 20.10.14

[combiz]

Could you please share your scflow_analysis.config file and the column names from your sample sheet? This looks like a parameter issue.

[MEFarhadieh]

Thanks for your reply.

I did my analysis with scFlow package in R. Everything was perfect. Thanks for developing these great tools.