The Metatranscriptome Assembly Pipeline

Summary

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.

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
• bryce911/spades:3.15.2
• microbiomedata/workflowmeta:1.1.1

Input files

The inputs for this workflow are as follows:

1. project name / contig prefix
2. Input fastq

{
  "metatranscriptome_assy.input_files":["./test_data/nmdc_xxxxxxx_filtered.fastq.gz"],
  "metatranscriptome_assy.proj_id":"nmdc:xxxxxxx"
}

Output files

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