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
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)