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nf-core / fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases
https://nf-co.re/fetchngs
MIT License
151 stars 73 forks source link

check out extensions for input files #256

Open maxulysse opened 10 months ago

maxulysse commented 10 months ago

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 commented 10 months ago

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 commented 1 month ago

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

sdhutchins commented 1 month ago

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).