DEMIC-in-cwl

A wrapper tool of DEMIC by CWL and Docker

Requirements

• Python3
• cwl-runner such as cwltool
• Docker
  • If you cannot use docker, this tool runs with --no-container options.
  • However, you have to install dependent tools of DEMIC, such as R, R libraries(reshape2, lme4, FactoMineR), and perl.

How to use

Before performing DEMIC, you have to assemble fragmented metagenome sequences, map reads, and bin them. See official instruction manual and its research manuscript.

With the CWL reference implementation (cwltool), toil-cwl-runner, or arvados-cwl-runner as your cwl-runner:

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           demic.cwl.cwl \
           --fasta_dir ${PATH_TO_FASTA_DIRECTORY} \
           --sam_dir  ${PATH_TO_SAM_DIRECTORY}

For other runners an input object is required:

inputs.yml

fasta_dir:
  class: Directory
  path: path/to/fasta_dir
sam_dir:
  class: Directory
  path: path/to/sam_dir

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           demic.cwl \
           inputs.yml

For other optional argument, please see the help message.

$cwl-runner demic.cwl --help

usage: demic.cwl [-h] --fasta_dir FASTA_DIR [--log LOG]
                 [--mapl_cutoff MAPL_CUTOFF] [--mapq_cutoff MAPQ_CUTOFF]
                 [--max_mismatch_ratio MAX_MISMATCH_RATIO]
                 [--output_dir_name OUTPUT_DIR_NAME] --sam_dir SAM_DIR
                 [--thread_num THREAD_NUM] [--window_size WINDOW_SIZE]
                 [--window_step WINDOW_STEP]
                 [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --fasta_dir FASTA_DIR
  --log LOG
  --mapl_cutoff MAPL_CUTOFF
                        cutoff of mapping length when calculating coverages
                        (default: 50)
  --mapq_cutoff MAPQ_CUTOFF
                        cutoff of mapping quality when calculating coverages
                        (default: 5)
  --max_mismatch_ratio MAX_MISMATCH_RATIO
                        maximum of mismatch ratio for each read as a hit
                        (default: 0.03)
  --output_dir_name OUTPUT_DIR_NAME
  --sam_dir SAM_DIR
  --thread_num THREAD_NUM
  --window_size WINDOW_SIZE
                        size (nt) of window for calculation of coverage
                        (default: 5000)
  --window_step WINDOW_STEP
                        step (nt) of window for calculation of coverage
                        (default: 100)