check out extensions for input files

[maxulysse]

Description of the bug

with -r 1.11.0

No extension fails as expected

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --input: string [id] does not match pattern ^\S+\.(csv|tsv|txt)$ (id)

but txt fails as well:

ERROR ~ Could not derive file type from /home/max/workspace/tests/id.txt. Please specify the file extension (CSV, TSV, YML and YAML are supported).

Command used and terminal output

No response

Relevant files

No response

System information

No response

[drpatelh]

Thanks @maxulysse ! Are you able to dig a little further to figure out why this is happening please?

Link to the pattern in the schema: https://github.com/nf-core/fetchngs/blob/04ee5031a4941b5fc52c158847cf797b45977965/nextflow_schema.json#L20

[cmatKhan]

Bump -- had the same thing happen. Submitted with .txt, same error as above, resubmitted with .tsv and it worked.

[sdhutchins]

I also had the same issue with version 1.12.0.

ERROR ~ Could not derive file type from /data/project/worthey_lab/external_data/pah/SRR_Acc_List.txt. Please specify the file extension (CSV, TSV, YML and YAML are supported).