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nf-core / metatdenovo

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
https://nf-co.re/metatdenovo
MIT License
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Unable to obtain DAG file. #265

Closed petemeng closed 8 months ago

petemeng commented 8 months ago

Description of the bug

nextflow run metatdenovo-1.0.0/main.nf --input samplesheet.csv --outfir result2 -profile docker -with-dag dag.html --skip_eukulele true
-[nf-core/metatdenovo] Pipeline completed successfully-
Completed at: 20-Feb-2024 18:50:32
Duration    : 1h 20m 57s
CPU hours   : 5.3
Succeeded   : 49

The command was run successfully, but no DAG file was obtained.

Command used and terminal output

No response

Relevant files

No response

System information

No response

### Tasks
erikrikarddaniel commented 8 months ago

The -with-dag parameter is a Nextflow parameter so should work for any pipeline. There is no code in this pipeline to deal with this.

I ran the metatdenovo test case with the parameter and it produced a diagram. Not very readable perhaps, but at least it worked.

Command: nextflow run nf-core/metatdenovo -r 1.0.0 -profile docker,test -with-dag dag.html

I note that you have misspelled --outdir in your example above. Moreover, you know that you don't need to clone or download the pipeline code? This is done automatically by Nextflow if you call it following my example above.

petemeng commented 8 months ago

The nextflow 23.10 version can generate dag files normally, but the nextflow 23.04 version can't generate.

erikrikarddaniel commented 8 months ago

OK, then I close this issue as it seems to be a Nextflow issue.