ERROR: Missing required column header -> sample

[kneubehl]

Description of the bug

I am getting an ERROR: Missing required column header -> sample however my input sample sheet has a sample column header and is formatted the same as in documentation.

ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (2023.7.17_taxprofiler_XXX_samples.csv)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (2023.7.17_taxprofiler_XXX_samples.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      2023.7.17_taxprofiler_XXX_samples.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  ERROR: Missing required column header -> sample. Note some columns can otherwise be empty. See pipeline documentation (https://nf-co.re/taxprofiler/usage).

Command error:
  ERROR: Missing required column header -> sample. Note some columns can otherwise be empty. See pipeline documentation (https://nf-co.re/taxprofiler/usage).

Work dir:
  /media/alex_2/XXX/2023.7.17_XXX_taxprofiler/work/4d/0fe87e531e8fea58baa465b7192c19

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

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

Command used and terminal output

nextflow run nf-core/taxprofiler --input 2023.7.17_taxprofiler_XXX_samples.csv --databases kraken2.csv --outdir 2023.7.17_taxprofiler_XXX_samples --run_kraken2 -profile docker --perform_shortread_qc --max_memory 200GB

Relevant files

2023.7.17_taxprofiler_XXX_samples.csv nextflow.log

System information

nextflow version 23.04.1.5866 hardware: Desktop, System76 Executor: local Container: docker OS: Pop!_OS 22.04 LTS nf-core/taxprofiler: nf-core/taxprofiler v1.0.1-g07b926a

[jfy133]

Could you check your CSV for hidden characters in the first line?

When I opened the CSV the sample column is sample

[kneubehl]

facepalm Sorry, I was pretty sure I checked for that, apparently not. Thanks.

[jfy133]

No worries! Glad it was easy fix!