matinnuhamunada
commented
1 month ago Hi WJ,
Glad to hear it works :)
The CLI for bgcflow run is just a simple wrapper of the snakemake CLI. So you can always directly use snakemake and use whatever parameter is available in snakemake documentation.
If you prefer to use the bgcflow_wrapper CLI, you can check what parameter is available using the help command, such as:
$ bgcflow run --help
Usage: bgcflow run [OPTIONS]
A snakemake CLI wrapper to run BGCFlow. Automatically run panoptes.
Options:
-d, --bgcflow_dir TEXT Location of BGCFlow directory. (DEFAULT: Current
working directory.)
--workflow TEXT Select which snakefile to run. Available
subworkflows: {BGC | Database | Report | Metabase |
lsagbc | ppanggolin}. (DEFAULT: workflow/Snakefile)
--monitor-off Turn off Panoptes monitoring workflow. (DEFAULT:
False)
--wms-monitor TEXT Panoptes address. (DEFAULT: http://127.0.0.1:5000)
-c, --cores INTEGER Use at most N CPU cores/jobs in parallel. (DEFAULT:
8)
-n, --dryrun Test run.
--unlock Remove a lock on the snakemake working directory.
--until TEXT Runs the pipeline until it reaches the specified
rules or files.
--profile TEXT Path to a directory containing snakemake profile.
-t, --touch Touch output files (mark them up to date without
really changing them).
-h, --help Show this message and exit.Note that the current bgcflow_wrapper package is using an older snakemake version and we are currently working on the update.
Also, there is another question. After bcgflow build report, the code '# use conda or mamba mamba env create -f bgcflow_notes.yaml # or r_notebook.yaml' doesn't work
I hope this means the command bgcflow build report works and you want to manually edit the notebook templates?
By snakemake convention, the environment files can be found in workflow/envs/<environment name>.yaml. Therefore, you can create the conda environment using mamba env create -f workflow/envs/bgcflow_notes.yaml.
You can actually reuse the conda environment built by snakemake by checking the snakemake log. They can be found in the .snakemake/conda folder.
PS: If you find any misleading or wrong instruction in the WIKI, please do let us know to correct it.
540889956
Hi, thanks for reaching out and using BGCFlow :)
I just wish to know how to use Custom input directory
To use custom input directory, you will need to set up two things:
project_config.yaml)samples.csvPlease find the example here: config.zip
This is how the project structure will look like:
And this is how the project configuration (
project_config.yaml) looks like:and finally, you need to add the custom sample in the
samples.csv:and you should get this message:
Why this workflow can still running after I delete all the input files?
I would assume that you don't change anything in the example template configuration and only deleted the default input files located in
data/raw. If this is the case, then the project can still run because all the samples are being fetched online from NCBI. You can check if this is the case from thesamples.csvThank you again for the question, we will be sure to add this to the FAQ section and improve the WIKI.