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

[cbravo93]

Describe the bug
single_sample_scrublet with different resolution parameters returns a loom file with only clustering for the last resolution listed

To Reproduce
Steps to reproduce the behavior:

1. Configure with these options:

singularity {
   cacheDir = '/ddn1/vol1/staging/leuven/stg_00002/lcb/lcb_projects/Pipeline_Dev/containers/'
   enabled = true
   autoMounts = true
   runOptions = '-B /ddn1/vol1/staging/leuven/stg_00002/,/staging/leuven/stg_00002/'
}

manifest {
   name = 'vib-singlecell-nf/vsn-pipelines'
   description = 'A repository of pipelines for single-cell data in Nextflow DSL2'
   homePage = 'https://github.com/vib-singlecell-nf/vsn-pipelines'
   version = '0.24.0'
   mainScript = 'main.nf'
   defaultBranch = 'master'
   nextflowVersion = '!20.04.1'
}

params {
   global {
      project_name = 'snRNA_Liver_Fresh_Mouse_5_Multiome_NST'
      outdir = 'out'
      species = 'mouse'
      genome {
         assembly = 'mm10'
      }
   }
   misc {
      test {
         enabled = false
      }
   }
   utils {
      container = 'vibsinglecellnf/utils:0.3.0'
      publish {
         compressionLevel = 6
         annotateWithBatchVariableName = false
      }
   }
   sc {
      file_converter {
         off = 'h5ad'
         tagCellWithSampleId = true
         useFilteredMatrix = true
         makeVarIndexUnique = false
      }
      scanpy {
         container = 'vibsinglecellnf/scanpy:0.5.2'
         report {
            annotations_to_plot = []
         }
         feature_selection {
            report_ipynb = '/src/scanpy/bin/reports/sc_select_variable_genes_report.ipynb'
            method = 'mean_disp_plot'
            minMean = 0.0125
            maxMean = 3
            minDisp = 0.5
            off = 'h5ad'
         }
         feature_scaling {
            method = 'zscore_scale'
            maxSD = 10
            off = 'h5ad'
         }
         neighborhood_graph {
            off = 'h5ad'
         }
         dim_reduction {
            report_ipynb = '/src/scanpy/bin/reports/sc_dim_reduction_report.ipynb'
            pca {
               method = 'pca'
               off = 'h5ad'
            }
            umap {
               method = 'umap'
               off = 'h5ad'
            }
            tsne {
               method = 'tsne'
               off = 'h5ad'
            }
         }
         clustering {
            preflight_checks = true
            report_ipynb = '/src/scanpy/bin/reports/sc_clustering_report.ipynb'
            method = 'leiden'
            resolutions = [0.4, 0.6, 0.8]
            off = 'h5ad'
         }
         marker_genes {
            method = 'wilcoxon'
            ngenes = 0
            groupby = 'leiden'
            off = 'h5ad'
         }
         filter {
            report_ipynb = '/src/scanpy/bin/reports/sc_filter_qc_report.ipynb'
            cellFilterStrategy = 'fixedthresholds'
            cellFilterMinNGenes = 350
            cellFilterMaxNGenes = 4000
            cellFilterMaxPercentMito = 0.05
            geneFilterMinNCells = 3
            off = 'h5ad'
            outdir = 'out'
         }
         data_transformation {
            method = 'log1p'
            off = 'h5ad'
         }
         normalization {
            method = 'cpx'
            countsPerCellAfter = 10000
            off = 'h5ad'
         }
      }
      scope {
         genome = 'mm10'
         tree {
            level_1 = 'VSN-pipeline'
            level_2 = 'Individual_samples'
            level_3 = ''
         }
      }
      scrublet {
         container = 'vibsinglecellnf/scrublet:0.1.4'
         doublet_detection {
            report_ipynb = '/src/scrublet/bin/reports/sc_doublet_detection_report.ipynb'
            useVariableFeatures = 'False'
            technology = '10x'
            off = 'h5ad'
         }
         cell_annotate {
            off = 'h5ad'
            method = 'obo'
            indexColumnName = 'index'
         }
         cell_filter {
            off = 'h5ad'
            method = 'internal'
            filters = [[id:'NO_DOUBLETS', sampleColumnName:'sample_id', filterColumnName:'scrublet__predicted_doublets', valuesToKeepFromFilterColumn:['False']]]
         }
      }
   }
   data {
      tenx {
         cellranger_mex = '/staging/leuven/stg_00002/lcb/lcb_projects/TEW/Multiome/cellranger_arc/TEW__ebb273__b33e6f__Multiome_Liver_CTRL_NSTprotocol/outs/'
      }
   }
   pcacv {
      container = 'vibsinglecellnf/pcacv:0.2.0'
      find_optimal_npcs {
         accessor = '@assays$RNA@scale.data'
      }
   }
}

process {
   executor = 'local'
   withLabel:'compute_resources__.*|compute_resources__default' {
      cpus = 2
      memory = '60 GB'
      time = '1h'
      clusterOptions = '-A lp_symbiosis'
   }
   withLabel:compute_resources__minimal {
      cpus = 1
      memory = '1 GB'
   }
   withLabel:compute_resources__mem {
      cpus = 4
      memory = '60 GB'
   }
   withLabel:compute_resources__cpu {
      cpus = 10
      memory = '60 GB'
   }
   withLabel:compute_resources__report {
      maxForks = 2
      cpus = 1
      memory = '60 GB'
   }
   withLabel:compute_resources__24hqueue {
      time = '24h'
   }
      withLabel:compute_resources__pcacv {
      cpus = 5
   }
}

timeline {
   enabled = true
   file = 'out/nextflow_reports/execution_timeline.html'
}

report {
   enabled = true
   file = 'out/nextflow_reports/execution_report.html'
}

trace {
   enabled = true
   file = 'out/nextflow_reports/execution_trace.txt'
}

dag {
   enabled = true
   file = 'out/nextflow_reports/pipeline_dag.svg'
}

min {
   enabled = false
}

2. Run using this entry point:

nextflow -C single_sample_scrublet.config run vib-singlecell-nf/vsn-pipelines -entry single_sample_scrublet

3. See error:

No error produced when running the pipeline. However, when checking the clusterings in the loom file there are only clusters for resolution 0.8 [no 0.4 nor 0.6]. All resolutions are computed though, and I have the corresponding notebooks.

Expected behavior
A loom file with all cluster resolutions, as I get with single_sample or single_sample_scenic. Normally I run single_sample_scrublet and single_sample_scenic and then append the scrublet results to the single_sample_scenic loom.

Please complete the following information:

• OS: [e.g. Ubuntu]
• Nextflow Version: [e.g. 20.04.1]
• vsn-pipelines Version: [e.g. 0.24.0]