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.
Description of the files:
.wdlfile: the WDL file for workflow definition.jsonfile: the example input for the workflow.conffile: the conf file for running Cromwell..shfile: the shell script for running the example workflow
-
fastq (illumina paired-end interleaved fastq)
-
contig prefix for fasta header
-
output path
-
input_interleaved (boolean)
-
forwards reads fastq file (required value when input_interleaved is false, otherwise use [] )
-
reverse reads fastq file (required value when input_interleaved is false, otherwise use [] )
-
memory (optional) ex: "jgi_metaASM.memory": "105G"
-
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.outdir":"/global/cfs/projectdirs/m3408/aim2/metagenome/assembly/ficus/503125_160870",
"jgi_metaASM.input_interleaved":true,
"jgi_metaASM.input_fq1":[],
"jgi_metaASM.input_fq2":[],
"jgi_metaASM.memory": "105G",
"jgi_metaASM.threads": "16"
}
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