BV BRC Assembly Task

Description:

This task assembles the input reads into an assembly using the BV-BRC CLI tools.

Steps

1. Logs into BV-BRC

2. Submits assembly job, waits for completion

3. Copies output from BV-BRC to wdl

4. Scans output for desired values

5. Compresses assembly file with Gzip

Docker:

andrewrlapointe/bvbrc

This docker includes the BV-BRC CLI as well as custom scripts to manage moving files to and from the BV-BRC workspace.

BV-BRC CLI Documentation found here.

Files Produced:

• <sample_name>_assembly_graph.plot.svg
• <sample_name>_AssemblyReport.html
• <sample_name>_contigs.fasta.gz
• <sample_name>_run_details.json
• contigs_workspace_path.txt
• timestamp.txt
• num_reads.txt
• average_read_depth.txt
• contigs_above_threshold.txt
• contigs_below_threshold.txt
• average_read_length.txt
• contig_fasta_file_size.txt