Skip to content
This repository has been archived by the owner on May 31, 2024. It is now read-only.

nf-core/sarek demo doesn't work due to the input validation error #587

Open
veselovamazon opened this issue Jan 6, 2023 · 0 comments
Open
Labels
bug Something isn't working

Comments

@veselovamazon
Copy link

Describe the Bug

The current input for the demo run doesn't work, because the current version of nf-core/sarek requires a csv file format.
For example:

NA21144,XX,0,NA21144,1,s3://1000genomes/phase3/data/NA21144/sequence_read/ERR251692_1.filt.fastq.gz,s3://1000genomes/phase3/data/NA21144/sequence_read/ERR251692_2.filt.fastq.gz

Steps to Reproduce

Execute sarek workflow for the project - https://github.com/aws/amazon-genomics-cli/tree/main/examples/nf-core-project

Relevant Logs

Jan-06 14:24:27.109 [main] ERROR nextflow.Nextflow - ERROR: Validation of pipeline parameters failed!
Jan-06 14:24:27.133 [main] ERROR nextflow.Nextflow - * --input: string [s3://healthai-public-assets-us-east-1/agc-demo-data/sarek/fastq_list.tsv] does not match pattern ^\S+.csv$ (s3://healthai-public-assets-us-east-1/agc-demo-data/sarek/fastq_list.tsv)

Expected Behavior

Actual Behavior

Screenshots

Additional Context

Operating System: macOS Monterey
AGC Version: 1.6.0
Was AGC setup with a custom bucket: no
Was AGC setup with a custom VPC: no

@veselovamazon veselovamazon added the bug Something isn't working label Jan 6, 2023
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant