Write automatic method

[SimonDMurray]

Based on the versions and flags, we wrtie a method

[SimonDMurray]

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/workflows/rnaseq.nf

[chriswyatt1]

https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/modules/nf-core/custom/dumpsoftwareversions/main.nf

I will try to implement this module from nf-core, which I think will run then adapt it into a method

[chriswyatt1]

OK, so I added the extra module (exactly,,,, I think), like in nf-core rnaseq, but the python script fails,

219f4ac

[chriswyatt1]

ERROR ~ Error executing process > 'CUSTOM_DUMPSOFTWAREVERSIONS (1)'

Caused by:
  Process `CUSTOM_DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (1)

Command executed [/Users/cwyatt/Desktop/synteny/./modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py]:

  #!/usr/bin/env python
  
  
  .....
  
  
  Command exit status:
  1

Command output:
  (empty)

Command error:
    File ".command.sh", line 61, in main
      versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/yaml/__init__.py", line 114, in load

    File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 152, in need_more_tokens
      self.stale_possible_simple_keys()
    File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 291, in stale_possible_simple_keys
      raise ScannerError("while scanning a simple key", key.mark,
  yaml.scanner.ScannerError: while scanning a simple key
    in "collated_versions.yml", line 19, column 5
  could not find expected ':'
    in "collated_versions.yml", line 20, column 1

Work dir:
  /Users/cwyatt/Desktop/synteny/work/f0/398067d6d56068efe4d619f403f6d9

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

[chriswyatt1]

Collated versions looks repetitive (even though we used .unique). its also malformed,,, maybe because of the VERSION print lines

"CHROMOPAINT":
    Python version: 3.10.13
    JCVI Version: 1.3.9
    Perl version: v5.36.0
"CHROMOPAINT":
    Python version: 3.10.13
    JCVI Version: 1.3.9
    Perl version: v5.36.0
"JCVI":
    Python version: 3.10.13
    JCVI Version: 1.3.9
"CHROMOPAINT":
    Python version: 3.10.13
    JCVI Version: 1.3.9
    Perl version: v5.36.0
    "SYNTENY":
        Python version: 3.10.13
        Perl version: v5.36.0
    END_VERSIONS
    R version 4.3.1 
    ggplot2 version: 2                   ggplot2      3.4.4
    ggstar version: 1.0.4
    pheatmap version: 1.0.12
    Perl version: v5.36.0
"CHROMOPAINT":
    Python version: 3.10.13
    JCVI Version: 1.3.9
       ```

[chriswyatt1]

I also need to add the following to the base.config:

    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
        publishDir = [
            path: { "${params.outdir}/pipeline_info" },
            pattern: '*_versions.yml'
        ]
    }