incomplete matches of variable name

[fruce-ki]

Description of the bug

I encountered an error that seems to be caused by the way variable names are matched between the contrasts and the samplesheet. The full error message is quoted in the next section as terminal output.

I have traced the issue to this awk call in NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS : awk -F'\t' '{print $'$column_number'}. At this point, $column_number has two values in it, since grep -En "^time" only matches the start of the variable name, resulting in both an exact match (time) and a partial match (timerat).

The error is fully resolved if I rename the variables, such that one is not a prefix of the other.

Command used and terminal output

-[nf-core/differentialabundance] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (time_W6_vs_W3.by_condition)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (time_W6_vs_W3.by_condition)` terminated with an error exit status (2)

Command executed:

  cls_file=time_W6_vs_W3.by_condition.cls
  
  column_number=$(cat samplesheet_linz.differentialabundance.sample_metadata.tsv | head -n 1 | tr '\t' "\n" | grep -En "^time" | awk -F':' '{print $1}')
  classes=$(tail -n +2 samplesheet_linz.differentialabundance.sample_metadata.tsv | awk -F'\t' '{print $'$column_number'}')
  unique_classes=$(echo -e "$classes" | awk '!x[$0]++')
  
  echo -e "$(echo -e "$classes" | wc -l) $(echo -e "$unique_classes" | wc -l) 1" > $cls_file
  echo -e "#$(echo -e "$unique_classes" | tr '\n' ' ')" | sed "s/ $//" >> $cls_file
  echo -e "$classes" | tr '\n' ' ' | sed "s/ $//" >> $cls_file
  echo -e "\n" >> $cls_file
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS":
      bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  awk: line 2: missing } near end of file

Relevant files

No response

System information

local execution on workstation with

Ubuntu 22.04

singularity 4.0.1-focal

nextflow 23.10

differentialabundance 1.4.0

[pinin4fjords]

Good spot! I've PR'd the module fix at nf-core/modules#4683 - feel free to make similar fixes yourself in future :-)