nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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3.16.x does not allow numeric sample ids #1419

Open idot opened 1 month ago

idot commented 1 month ago

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

idot commented 1 month ago

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

idot commented 1 month ago

is indeed an issue. added pull request