Tiling-NF pipeline

A pipeline for pathology slide analysis: tile and detect tissue

Requirements

• Unix-like operating system
• Java 11

Quickstart

1. Install anaconda or Mamba

2. Install nextflow:

   curl -s https://get.nextflow.io | bash
   

3. Launch the pipeline execution using docker

   ./nextflow run msk-mind/tiling-nf --samples_csv samples.csv
   

   samples.csv is a csv file which has a url (specify with --slide_url_column) column that has the path to the slide

4. When the execution completes, meta.csv will be in the results (specify with --outdir) directory

Azure Batch Support

1. Create an Azure storage account and batch account.

2. Modify the nextflow configuration files as necessary (see https://www.nextflow.io/docs/edge/azure.html)

3. Set the necessary secrets using nextflow secrets set. At a minimum set AZURE_BATCH_KEY and AZURE_STORAGE_KEY.

4. Launch nextflow:

   nextflow -Dcom.amazonaws.sdk.disableCertChecking=true run main.nf -bucket-dir {azure_bucket_dir} -profile standard,cloud
   

   where {azure_bucket_dir} is an azure path like az://test/nftest.

5. When the execution completes, meta.csv will be in the results directory