Fix GroHMM on full runs

[edmundmiller]

Samplesheet:

sample,fastq_1,fastq_2
GM0h_REP1,../data/groseq_raw/GM0h.fastq.gz,

Data available here:

Error:

Caused by:
  Process `NFCORE_NASCENT:NASCENT:GROHMM:GROHMM_TRANSCRIPTCALLING (GM0h)` terminated with an error exit status (1)

Command executed:

  transcriptcalling_grohmm.R \
      --bam_file GM0h.sorted.bam \
       \
      --outprefix GM0h \
      --gtf genes.gtf \                                                                                          --outdir ./ \
      --cores 12 \


  cat <<-END_VERSIONS > versions.yml
  "NFCORE_NASCENT:NASCENT:GROHMM:GROHMM_TRANSCRIPTCALLING":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      bioconductor-grohmm: $(Rscript -e "library(groHMM); cat(as.character(packageVersion('groHMM')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in Fp[[i]] + 1 : non-numeric argument to binary operator
  Calls: detectTranscripts
  In addition: Warning messages:
  1: In mclapply(readsList, function(x) { :
    all scheduled cores encountered errors in user code
  2: In mclapply(readsList, function(x) { :
    all scheduled cores encountered errors in user code
  Execution halted

Work dir:
  /petastore/ganymede/home/eam150030/nascent/work/f0/e794715b51ad2b1036c36c8fb7b410

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`