allow integer sample names

[idot]

int was not allowed as sample name anymore (since 3.16.0) Validation of file failed: -> Entry 1: Error for field 'sample' (298098): Sample name must be provided and cannot contain spaces

PR checklist

• [*] This comment contains a description of changes (with reason).

• [ ] CHANGELOG.md is updated.

[github-actions[bot]]

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2. Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[idot]

fixes #1419

[pinin4fjords]

@idot can you confirm that you've tested the workflow with this change? Also, please update the CHANGELOG.

[idot]

I have updated the changelog. There was a discussion on slack and the developers wanted a more comprehensive solution however in 3.18.0 the error is still there. I have tested also 3.18 with this change.

[pinin4fjords]

Mind that R does not allow purely numeric column names. If you try assigning one, it will be automatically prepended with X:

> example <- data.frame("123345"=LETTERS)
> head(example)
  X123345
1       A
2       B
3       C
4       D
5       E
6       F

So you will anyway end up with non-numeric sample names in your quantification and I would want to perform a very careful review of all R scripts, whether some data merging steps fail, e.g. the scaling/normalization just defaults to 1 for each sample etc.

I fear there might be more subtle issues that do not show instantly by a crashing pipeline run.

I did at some point go through and put check.names = FALSE in various places to avoid this.

@idot said that they had test this, so fingers crossed that was effective.

[idot]

Yes, in the R part the sample names get an X prepended

[pinin4fjords]

Yes, in the R part the sample names get an X prepended

OK, then we need to do some work to address that before this is merged.