Error in exploratory plots with --differential_subset_to_contrast_samples

[sci-kai]

Description of the bug

Hi, I ran the nf-core differentialabundance pipeline with nf-core/rnaseq output, 6 different contrasts defined in contrasts.csv and the parameter --differential_subset_to_contrast_samples .
I get the following error message (I removed the samplenames for privacy reasons):

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (condition)` terminated with an error exit status (1)


Command executed:

  exploratory_plots.R \
      --sample_metadata "samplesheet.sample_metadata.tsv" \
      --feature_metadata "Homo_sapiens.anno.feature_metadata.tsv" \
      --assay_files "salmon.merged.gene_counts.assay.tsv,all.normalised_counts.tsv,all.vst.tsv" \
      --contrast_variable "condition" \
      --outdir "condition" \
      --sample_id_col "sample" --feature_id_col "gene_id" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1" --log2_assays "raw,normalised"
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."

Command error:
      table, tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:utils’:
  
      findMatches
  
  The following objects are masked from ‘package:base’:
  
      expand.grid, I, unname
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: ‘Biobase’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      rowMedians
  
  The following objects are masked from ‘package:matrixStats’:
  
      anyMissing, rowMedians
  
  
  Attaching package: ‘shinyngs’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      colMedians
  
  The following object is masked from ‘package:matrixStats’:
  
      colMedians
  
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'object' in selecting a method for function 'na.omit': Some sample metadata names ({here was a list of samplenames}
  Calls: lapply -> lapply -> FUN -> na.omit -> read_matrix
  Execution halted
  INFO:    Cleaning up image...

Work dir:
  /differentialabundance_subsetcontrasts/work/6a/8581fed49925b45df360cb03bf6bd0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

I found the error to be the following:
The samplesheet.sample_metadata.tsv contains all samplenames, while the normalised counts file all.normalised_counts.tsv only contains samples that are defined as contrasts.
Line 190 in the exploratory_plots.R file therefore gives an error, as the assay file has less columns as specified in sample_metadata.

assay_data <- lapply(assay_files, function(x) {
  na.omit(
    read_matrix(
      x,
      sample_metadata = sample_metadata,
      feature_metadata = feature_metadata,
      row.names = 1
    )
  )
})

I propose a solution could be to subset the samplesheets for each contrast when --differential_subset_to_contrast_samples is enabled and supply to this process.

Command used and terminal output

nextflow run nf-core-differentialabundance_1.5.0/1_5_0 \
-profile singularity,hilbert,offline \
-c config/differentialabundance/run-differentialabundance.config \
-params-file config/differentialabundance/nf-params.json \
-plugins [email protected] \
--differential_subset_to_contrast_samples

Relevant files

nf-params.json:

{
  "study_name": "mosaik",
  "input": "config/differentialabundance/samplesheet.csv",
  "contrasts": "config/differentialabundance/contrasts.csv",
  "outdir": "results",
  "matrix": "results_summary/salmon.merged.gene_counts.tsv",
  "transcript_length_matrix": "results_summary/salmon.merged.gene_lengths.tsv",
  "gsea_run": true,
  "gsea_zip_report": true,
  "gene_sets_files": "db/msigdb/merged/c1_c2cp_c5hpo_c5gobp.v2024.1.Hs.symbols.gmt",
  "genome": "GRCh38",
  "gtf": "db/rnaseq_ensemble_reference/Homo_sapiens.GRCh38.112.gtf.gz"
}

profile hilbert & offline:

  hilbert {
        params {
            config_profile_description = 'HILBERT'
            // HPC job resources
            max_memory = 200.GB
            max_cpus = 32
            max_time = 72.h
        }
        process {
            executor = 'pbspro'
            module = 'Singularity/3.7.1'
            queuesize = 100
        }
    }
    offline {
        // reduce the pulltimeout so that you don't need to wait 20 minutes for error message of failed singularity pullTimeout (if workflow accidentally tries to do so)
        apptainer.pullTimeout = '1s'
        singularity.pullTimeout = '1s'
        charliecloud.pullTimeout = '1s'
    }

System information

nextflow version: 24.04.4
version: 1.5.0