Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

check out extensions for input files #256

Open
maxulysse opened this issue Jan 25, 2024 · 3 comments
Open

check out extensions for input files #256

maxulysse opened this issue Jan 25, 2024 · 3 comments
Labels
bug Something isn't working

Comments

@maxulysse
Copy link
Member

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

@maxulysse maxulysse added the bug Something isn't working label Jan 25, 2024
@drpatelh
Copy link
Member

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:

"pattern": "^\\S+\\.(csv|tsv|txt)$",

@cmatKhan
Copy link

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

@sdhutchins
Copy link

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).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

4 participants