Hi! I am getting an error during `'NFCORE_CIRCRNACIRCRNAMIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)'`:

ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS (batch_1)` terminated with an error exit status (1)


Command executed [/home/azabala/.nextflow/assets/nf-core/circRNA/./workflows/circrna/../../subworkflows/local/../../modules/local/compute_correlations/templates/compute_correlations.R]:

  #!/usr/bin/env Rscript
  
  library(fishpond)
  suppressMessages(library(SummarizedExperiment))
  
  tx_expression <- readRDS('experiments.merged.rds')
  mi_expression <- read.table('mirna.normalized_counts_filtered.tsv', header=TRUE, row.names=1, sep='\t')
  interactions <- read.table('mirna.targets.1.tsv', sep='\t')
  
  tx_expression <- scaleInfReps(tx_expression)
  tx_expression <- labelKeep(tx_expression) # Here one can perform custom filtering
  
  if (!any(mcols(tx_expression)$keep)) {
      stop('No transcripts left after filtering')
  }
  
  result_cols <- c('stat', 'log2FC', 'pvalue', 'locfdr', 'qvalue')
  
  # Iterate rows of interactions
  for (i in 1:nrow(interactions)) {
      # Get miRNA and target gene
      miRNA <- interactions[i, 1]
      targets <- unlist(strsplit(interactions[i, 2], ','))
  
      mirna_expression <- mi_expression[miRNA,]
      transcript_expression <- tx_expression[targets,]
  
      if (!any(mcols(transcript_expression)$keep)) {
          print(paste('No transcripts left after filtering for miRNA', miRNA))
          next
      }
  
      # Add miRNA expression to colData so that it can be used for correlation
      colData(transcript_expression) <- cbind(
          colData(transcript_expression),
          t(mirna_expression[, rownames(colData(transcript_expression))])
      )
  
      result <- rowData(swish(transcript_expression, miRNA, cor = "pearson"))[, result_cols]
      result <- result[complete.cases(result), ]
      write.table(result, paste0(miRNA, '.tsv'), sep = '\t')
  }
  
  ################################################
  ################################################
  ## VERSIONS FILE                              ##
  ################################################
  ################################################
  
  r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
  
  writeLines(
      c(
          '"NFCORE_CIRCRNA:CIRCRNA:MIRNA_PREDICTION:COMPUTE_CORRELATIONS":',
          paste('    r-base:', r.version)
      ),
  'versions.yml')
  
  ################################################
  ################################################
  ################################################
  ################################################

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 't': undefined columns selected
  Calls: cbind ... standardGeneric -> eval -> eval -> eval -> t -> [ -> [.data.frame
  Execution halted

Work dir:
  /scratch/azabala/network/circRNA/work_circRNA/fb/8cd9537a6b1538f793cd1c4367e95d

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

Hey, can you open an issue on github? There it's less likely for me to forget it

Thanks, Nico

I am currently doing an internship, which is why I can't maintain all my pipelines properly. But this is my last week, the week after I will be on vacation, but then I'll be back to business