Error executing process > 'NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_FILTER_SAME_GENE (rna_s1221_S42)'

Caused by:
  Missing output file(s) `*.fusions.tsv` expected by process `NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_FILTER_SAME_GENE (rna_s1221_S42)` (note: input files are not included in the default matching set)


Command executed:

  # Filter out same-gene fusions (gene1==gene2); keep header and inter-gene rows only.
      # Write to temp file first since input and output can have the same path (avoid truncating input).
      awk -F'	' '
      NR==1 {
          for(i=1;i<=NF;i++) {
              if ($i=="#gene1" || $i=="gene1") g1=i;
              if ($i=="gene2") g2=i;
          }
          print $0;
          next;
      }
      (g1+0 && g2+0) && ($g1 != $g2) { print $0 }
      ' "rna_s1221_S42.arriba.fusions.tsv" > rna_s1221_S42.arriba.fusions.tsv.tmp
      mv rna_s1221_S42.arriba.fusions.tsv.tmp rna_s1221_S42.arriba.fusions.tsv
  
      cat <<-END_VERSIONS > versions.yml
      "NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_FILTER_SAME_GENE":
          awk: "filter same-gene (gene1==gene2)"
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/5f12ba166f9a11194361da04e91e83

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/biocontainers/pandas:1.5.2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line