3.3: Sample sheet error check false positive

[mjsteinbaugh]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/rnaseq pipeline documentation

Description of the bug

Seeing a weird false positive error message for the samplesheet.csv checker.

ERROR: Please check samplesheet header -> sample,fastq_1,fastq_2,strandedness != sample,fastq_1,fastq_2,strandedness

Steps to reproduce

nextflow run 'nf-core/rnaseq' \
    -r '3.3' \
    -profile 'docker' \
    --aligner 'star_salmon' \
    --genome 'GRCh38' \
    --input 'samplesheet.csv'

Expected behaviour

These columns match the current recommendations in the documentation.

[mjsteinbaugh]

Figured this out, bad CSV conversion from Excel. Need to resave in UTF-8 (no BOM), Unix LF instead of Windows CRLF. The error message could be improved to detect this.

[drpatelh]

Hi @mjsteinbaugh ! Thanks for reporting. This has come up a few times now but it's difficult to test and reproduce. Be great if you are able to reproduce and upload the samplesheet here. Failing that I can try to push a tentative fix to see if it resolves the issue for you locally.

[mjsteinbaugh]

Sure thing I'll make a couple of minimal examples that fail and will post them here.

[mjsteinbaugh]

@drpatelh Saw your post on Slack, I'll follow up when I have some free time