Duke-GCB/MMAP-cwl

Name: MMAP-cwl

Owner: Duke Center for Genomic and Computational Biology

Description: Common Workflow Language tool and workflow definitions for MMAP pipeline

Created: 2015-08-07 19:09:31.0

Updated: 2015-11-10 18:47:13.0

Pushed: 2015-12-21 15:05:05.0

Homepage: null

Size: 29

Language: Shell

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README

MMAP-cwl

Common Workflow Language tool and workflow definitions for MMAP pipeline

Implementation of MMAP pipeline using CWL, leveraging docker images built under MMAP-Docker for docker-pipeline

First-time setup

1. Install Docker
2. Install the CWL Reference Implementation
3. Clone this repo
4. Generate a BLAST+ database of the GO sequences, using makeblastdb-go
5. Write a job definition JSON file, like this example
6. Set the path of the input_fasta_file to the file containing the data to analyze
7. Set the path of the blast_db_dir to the directory containing your BLAST+ database
8. Set the name of the output_goterms_file_name to your desired output file name

Running

cwl-runner /path/to/mmap-cwl/mmap.cwl mmap.json