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:
.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 workflowfastq (illumina paired-end interleaved fastq)
contig prefix for fasta header
project name
resource where run the workflow
informed_by
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.proj":"nmdc:503125_160870",
"jgi_metaASM.resource": "NERSC -- perlmutter",
"jgi_metaASM.informed_by": "nmdc:xxxxxx",
"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