Nextflow Run from Git: Get the Tag into Script/Pipeline

[tjdurant]

Hi All,

When running pipelines, our group runs them from a gitlab repo using a tag:

nextflow run <private repo> -profile docker --batch_id <batch_id> -r <tag_version>

We would like to pull the <tag_version> into the pipeline and output it in a file.

Does anyone know if that is possible?

Or, what do other people do? I know we can update the config manifest to include the version, but we've had instances were developers have forgotten to update the config file.

Any thoughts/comments/suggestions are welcome.

Thanks!
Tom

[pditommaso]

You can use -with-report option that track that info.

Even better you can use the -with-tower option that will upload those info to https://tower.nf/

[tjdurant]

thank you @pditommaso!

One follow-up question, do you (or other community members), have recommendations on how to pass this report to the pipeline output directory if the output paths are defined in the nextflow.config file?

[pditommaso]

make a wrapper script to handle it!

[tjdurant]

thanks, any good examples out there that you know of?

[pditommaso]

#!/bin/bash
nextflow run <YOUR PIPELINE> -with-report 
cp report.html /some/where

[tjdurant]

We ended up defining the path to the report in the report scope

report {
    file = "${params.project_root_dir}/COVID_SEQ_${params.pipeline_version}/BATCH_${params.batch_id}_${params.bed_version}/pipeline_output_summary/nextflow_pipeline_report.html"
}

[stevekm]

This seems to work when the pipeline is started from a remote repository (nextflow run somerepo/somepipeline) but it does not seem to work if Nextflow is run directly from within the repo (nextflow run main.nf)
would be helpful if Nextflow could report the output from something like git describe (e.g. 1.16-6-g934775a) and use that within the pipeline for reporting