This workflow is developed by Brian Foster at JGI. Original repo can be found here. This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads.
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 inputs for this workflow are as follows:
- project name / contig prefix
- Input fastq
{
"metatranscriptome_assy.input_files":["./test_data/nmdc_xxxxxxx_filtered.fastq.gz"],
"metatranscriptome_assy.proj_id":"nmdc:xxxxxxx"
}
The output will have one directory named by prefix project name and a bunch of output files, including statistical numbers, status log, and run information.
The main read count table output is named by prefix.pairedMapped_sorted.bam
.
|-- nmdc_xxxxxxx_bamfiles.tar
|-- nmdc_xxxxxxx_contigs.fna
|-- nmdc_xxxxxxx_pairedMapped.sam.gz
|-- nmdc_xxxxxxx_pairedMapped_sorted.bam
|-- nmdc_xxxxxxx_readlen.txt
|-- nmdc_xxxxxxx_scaffolds.fna
|-- nmdc_xxxxxxx_spades.log
|-- scaffold_stats.json