Basic concepts

--------------------------------------- out_json_parser.py --------------------------------------
Script out_json_parser.py parses output JSON structure after first step.
If QC-PASSED file was found, script adds extra lines to YML file (that would be used for second part of pipeline)

For assembly (mode (-m) "assembly")
  + filtered_fasta
For raw-reads (mode (-m) "raw-reads")
  + filtered_fasta
  + motus_input
--------------------------------------- Assembly --------------------------------------------------

Assembly folder has 2 files: assembly--1.cwl (before qc) and assembly-2.cwl (after qc)
assembly-pipeline-v.5-qc.cwl == -.cwl + assembly-2.cwl

>>>>>> Schema:

   Run assembly--1.cwl
           |
    Check qc-status
    /                \
 QC-PASSED          QC-FAILED
   |                      |
 run assembly-2.cwl      /
   |                    /
  move first part to output folder
   |
  move second part to output folder


---------------------------------------- Raw reads ------------------------------------------------
raw-reads-paired-1.cwl == seq-prep + raw-reads-single-1.cwl
raw-reads-2.cwl - common for paired and single pipeline

raw-reads-single-pipeline-v.5-qc.cwl == raw-reads-single-1.cwl + raw-reads-2.cwl
raw-reads-paired-pipeline-v.5-qc.cwl == raw-reads-paired-1.cwl + raw-reads-2.cwl

>>>>>> Schema:

single                              paired
  |                                    |
raw-reads-single-1.cwl            raw-reads-paired-1.cwl
                \                    /
                    check qc-status
                      /         \
             QC-PASSED         QC-FAILED
                 |                |
         raw-reads-2.cwl          |
                  \              /
            move first part to output folder
                   |
            move second part to output folder