In Snakemake, can I include the `--use-conda` flag in a workflow profile? - Stack Overflow

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I am using a workflow profile saved in profiles/default/config.yaml to define default values for my snakemake command line arguments. I use conda to manage my environments, and so my snakemake calls usually include

snakemake --use-conda --conda-prefix='path.to.conda.envs'

In my config.yaml I can define the --conda-prefix parameter, but the --use-conda parameter is just a flag with no value. How does one define that in the YAML? The YAML takes key:value inputs and translates those into --key=value. I have not been able to find a way to input key and have it return just --key. For example, in my config.yaml:

# `--conda-prefix` works, since this is a traditional key:value pair
conda-prefix: 'path.to.conda.envs'

# None of these variations work to define `--use-conda`
use-conda: TRUE   ##Does not work because `--use-conda=TRUE` is not valid
use-conda: ~      ##This does not produce an error, but it does not pass `--use-conda` correctly and conda is not used
use-conda         ##Is not valid YAML syntax

Is there a way to do this, or do I just have to always specify --use-conda in the command line?

I am using a workflow profile saved in profiles/default/config.yaml to define default values for my snakemake command line arguments. I use conda to manage my environments, and so my snakemake calls usually include

snakemake --use-conda --conda-prefix='path.to.conda.envs'

In my config.yaml I can define the --conda-prefix parameter, but the --use-conda parameter is just a flag with no value. How does one define that in the YAML? The YAML takes key:value inputs and translates those into --key=value. I have not been able to find a way to input key and have it return just --key. For example, in my config.yaml:

# `--conda-prefix` works, since this is a traditional key:value pair
conda-prefix: 'path.to.conda.envs'

# None of these variations work to define `--use-conda`
use-conda: TRUE   ##Does not work because `--use-conda=TRUE` is not valid
use-conda: ~      ##This does not produce an error, but it does not pass `--use-conda` correctly and conda is not used
use-conda         ##Is not valid YAML syntax

Is there a way to do this, or do I just have to always specify --use-conda in the command line?

• conda
• snakemake

Share Improve this question Follow asked Mar 12 at 18:04 Sean TaylorSean Taylor 2333 bronze badges

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1 Answer 1

Sorted by: Reset to default 1

You want:

use-conda: true

It has to be lower case. You might think it would be use-conda: True because we have to use True and False in Python code, but in YAML it's all lowercase. Any other variant like TRUE is treated as a string.

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