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nf-cwl-wrap

Introduction

nf-cwl-wrap is a Nextflow wrapper for CWL workflows. It uses cwltool to execute workflows and can be used both locally and on Nextflow Tower.

Workflow Summary

nf-cwl-wrap takes a .cwl workflow file (cwl_file) and a .csv input file (s3_file). The .csv file is expected to be in the following format:

data_file,input_file
s3://iatlas-project-tower-bucket/iatlas_fpkm.tsv,s3://iatlas-project-tower-bucket/immune_subtype_clustering_input.json

It should contain paths to a data_file - the input data for the CWL workflow, and an input_file - a .json or .yaml file containing the required metadata for the CWL workflow run. The s3_file can contain multiple rows in this format. It will create a channel for each row and execute the CWL workflow on the files provided in parallel. Outputs are stored in the working directory for each process execution.

The s3_file format is compatible with nf-synstage so that users can first stage their data_file's and input_file's in S3 buckets ahead of Nextflow Tower runs with this repository.

Quick Start

  1. Install Nextflow (>=22.10.1)
  2. Install Docker
  3. Download this workflow and test it with the default parameters using:
nextflow run main.nf
  1. Run your own workflows:
nextflow run main.nf --cwl_file YOUR_CWL_FILE --input_file YOUR_INPUT_FILE