Running error

[aslangabriel]

Description of the bug

Hi, I ran the command "nextflow run xiaoli-dong/pathogenseq -r 5a4a403 --input samplesheet.csv -profile docker --outdir results --platform illumina --skip_illumina_dehost true", it always displayed the error of "Project xiaoli-dong/pathogenseq contains uncommitted changes -- Cannot switch to revision: 5a4a403". I have tested all the measures including "nextflow clean -f
and nextflow self-update
". They didn't work. Would you like to help me fix this?

Command used and terminal output

No response

Relevant files

No response

System information

ubuntu22.04

[MohdKhairulNizam]

Hi,
I would suggest you to download the git repo into your local directory and run the pipeline using:

nextflow run pathogenseq/main.nf -input samplesheet.csv -profile docker --outdir results --platform illumina --skip_illumina_dehost true