This pipeline aims at providing a heavily parallelized equivalent to the Spapros package for probeset selection.
A runnable example is provided in the run.sh script. We will provide more details and documentation as the project progresses.
Usage:
The typical command for running the pipeline is as follows:
nextflow run . -profile conda --adata data/small_data_raw_counts.h5ad --parameters data/parameters.yml --probeset data/selections_genesets_1.csv --markers data/small_data_marker_list.csv --probeset_ids genesets_1_0,genesets_1_1
Mandatory arguments:
--adata [file] Path to h5ad file containing the single-cell data
--parameters [file] Path to a parameters file. See Spapros documentation
--probeset [file] Path to the selected probesets as determined by Spapros. See Spapros documentation.
--markers [file] Path to a file containing the marker genes
--probeset_ids [str] Comma separated list of probesets to evaluate
-profile [str] Configuration profile to use. Can use multiple (comma separated)
Available: docker, singularity, test, awsbatch and more
Evaluation:
--run_cs [bool] Whether to run cluster similarity evaluation (true)
--run_knn [bool] Whether to run KNN graph evaluation (true)
--run_rf [bool] Whether to run random forest evaluation (true)
--run_corr [bool] Whether to run correlation evaluation (true)
Other options:
--outdir [file] The output directory where the results will be saved
--email [email] Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
--email_on_fail [email] Same as --email, except only send mail if the workflow is not successful
-name [str] Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic
AWSBatch options:
--awsqueue [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion [str] The AWS Region for your AWS Batch job to run on
--awscli [str] Path to the AWS CLI tool