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3.16.x does not allow numeric sample ids #1419

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idot opened this issue Oct 17, 2024 · 2 comments
Open

3.16.x does not allow numeric sample ids #1419

idot opened this issue Oct 17, 2024 · 2 comments
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@idot
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idot commented Oct 17, 2024

Description of the bug

Hello,
a samples.csv that was working in 3.15.1 is not accepted anymore.
The file has numeric sample ids. Prepending them with x makes it work again.
However numeric sample ids are very common and there is no reason that they should not be valid.

* --input (/users/ido.tamir/work/analysis/rnaseq/ribozero_align_20241017.csv): Validation of file failed:
        -> Entry 1: Error for field 'sample' (298098): Sample name must be provided and cannot contain spaces
        -> Entry 2: Error for field 'sample' (298504): Sample name must be provided and cannot contain spaces
        -> Entry 3: Error for field 'sample' (317960): Sample name must be provided and cannot contain spaces
        -> Entry 4: Error for field 'sample' (319093): Sample name must be provided and cannot contain spaces
        -> Entry 5: Error for field 'sample' (297292): Sample name must be provided and cannot contain spaces
        -> Entry 6: Error for field 'sample' (320543): Sample name must be provided and cannot contain spaces

Command used and terminal output

nextflow run -r 3.16.1 nf-core/rnaseq --input test.csv --genome hg38 --outdir .

Relevant files

test.csv

System information

  • nextflow 24.04.4
  • HPC
  • slurm
  • Singularity
  • Linux
  • nf-core/rnaseq 3.16.0,3.16.1
@idot idot added the bug Something isn't working label Oct 17, 2024
@idot
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idot commented Oct 17, 2024

There must be some wierd invisible characters in the file. Another file with only numeric ids did work.

@idot idot closed this as completed Oct 17, 2024
@idot idot reopened this Oct 18, 2024
@idot
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idot commented Oct 18, 2024

is indeed an issue. added pull request

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