Right now only one round of diffmeth is incorporated into the report

[alexg9010]

Right now only one round of diffmeth is incorporated into the report

[Blosberg]

When I submit as follows:

  differential-methylation:
    cores: 20
    treatment-groups:
      - ['0', '1'],
        ['0', '2']
    annotation:
...

I get the following errors:

$ ./pigx-bsseq test/samplesheet.csv -s test/settings.yaml  
Traceback (most recent call last):
  File "./pigx-bsseq", line 402, in <module>
    args.settings)
  File "./pigx-bsseq", line 236, in generate_config
    update_config(settings,yaml.safe_load(open(settingsfile, 'r')))

So I guess the first thing to clarify is what the right syntax is to enter multiple treatments.

[rekado]

Groups have to be specified as arrays. In YAML that's done like this:

  differential-methylation:
    cores: 20
    treatment-groups:
      - ['0', '1']
      - ['0', '2']
    annotation:
...

An alternative is to use JSON syntax (which we already do for the groups themselves), i.e. square brackets for arrays/lists.

[Blosberg]

We decided that to solve this issue, it's ok to have differential methylation output a separate html report for each comparison. I'd recommend adding such an html file to the OUTPUT_FILES for each treatment group, and then just have the rule run arbitrarily many times.

Is that the approach? I'm just wondering what the status of this is.

[alexg9010]

Yes, exactly. If I remember correctly I asked Kasia to take over, so you might ask her if she already made progress on this.

[katwre]

sorry guys, I didn't see your msgs! I took over this issue