The Metagenome Assembly Pipeline

Summary

This workflow is developed by Brian Foster at JGI and original from his repo. It take paired-end reads runs error correction by bbcms (BBTools). The clean reads are assembled by MetaSpades. After assembly, the reads are mapped back to contigs by bbmap (BBTools) for coverage information.

Running Workflow in Cromwell

Description of the files:

• .wdl file: the WDL file for workflow definition
• .json file: the example input for the workflow
• .conf file: the conf file for running Cromwell.
• .sh file: the shell script for running the example workflow

The Docker image and Dockerfile can be found here

microbiomedata/bbtools:38.96

microbiomedata/spades:3.15.0

Input files

1. fastq (illumina paired-end interleaved fastq)

2. contig prefix for fasta header

3. project name

4. resource where run the workflow

5. informed_by

6. memory (optional) ex: "jgi_metaASM.memory": "105G"

7. threads (optional) ex: "jgi_metaASM.threads": "16"

{
  "jgi_metaASM.input_file":"/global/cfs/projectdirs/m3408/ficus/11809.7.220839.TCCTGAG-ACTGCAT.fastq.gz",
  "jgi_metaASM.rename_contig_prefix":"503125_160870",
  "jgi_metaASM.proj":"nmdc:503125_160870",
  "jgi_metaASM.resource": "NERSC -- perlmutter",
  "jgi_metaASM.informed_by": "nmdc:xxxxxx",
  "jgi_metaASM.memory": "105G",
  "jgi_metaASM.threads": "16"
}

Output files

Below is a part list of all output files. The main assembly contigs output is in final_assembly/assembly.contigs.fasta.

	├── bbcms
	│   ├── berkeleylab-jgi-meta-60ade422cd4e
	│   ├── counts.metadata.json
	│   ├── input.corr.fastq.gz
	│   ├── input.corr.left.fastq.gz
	│   ├── input.corr.right.fastq.gz
	│   ├── readlen.txt
	│   └── unique31mer.txt
	├── final_assembly
	│   ├── assembly.agp
	│   ├── assembly_contigs.fna
	│   ├── assembly_scaffolds.fna
	│   └── assembly_scaffolds.legend
	├── mapping
	│   ├── covstats.txt (mapping_stats.txt)
	│   ├── pairedMapped.bam
	│   ├── pairedMapped.sam.gz
	│   ├── pairedMapped_sorted.bam
	│   └── pairedMapped_sorted.bam.bai
	└── spades3
		├── assembly_graph.fastg
		├── assembly_graph_with_scaffolds.gfa
		├── contigs.fasta
		├── contigs.paths
		├── scaffolds.fasta
		└── scaffolds.paths