nf-core/rnaseq

3.16.x does not allow numeric sample ids

Opened this issue · 3 comments

idot commented

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 commented

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

idot commented

is indeed an issue. added pull request

idot commented

The error persists in 3.18.0:

      -> Entry 1: Error for field 'sample' (343851): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)
        -> Entry 2: Error for field 'sample' (343852): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)
        -> Entry 3: Error for field 'sample' (343853): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)
        -> Entry 4: Error for field 'sample' (343854): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)
        -> Entry 5: Error for field 'sample' (343855): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)