Overly long string size in input samplesheet causes samplesheet check to erroenously report missing header

[microbemarsh]

Description of the bug

When trying to run funcscan with more than 2 samples causes the pipeline to fail. slack channel thread

Command used and terminal output

nextflow run nf-core/funcscan --input funcscan_SLR25hyb.csv --outdir SLR25_hyb -profile docker --run_amp_screening --run_arg_screening --run_bgc_screening --amp_skip_amplify --arg_skip_deeparg --amp_skip_hmmsearch --bgc_skip_hmmsearch -r 1.0.0

######################################################################################

 Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:INPUT_CHECK:SAMPLESHEET_CHECK (funcscan_SLR25hyb.csv)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:INPUT_CHECK:SAMPLESHEET_CHECK (funcscan_SLR25hyb.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      funcscan_SLR25hyb.csv \
      samplesheet.valid.csv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  [CRITICAL] The given sample sheet does not appear to contain a header.

Relevant files

Link to 6 mags and csv file

System information

Nextflow version 22.10.6.5843
Local Server
Local
Docker
Ubuntu Linux
nf-core/funcscan -r 1.0.0

[jfy133]

After a bit of experimenting (see end of the slack message above) it seems that if we reduce the number of new lines to check in the samplesheet_check.py down to 2 in the read_head() function, it then works.

@Midnighter believes he may have actually found a bug in python itself (:scream: ), and possibly suggests it might be easier to just use pandas for all of this...