Datavzrd report

[tedil]

This PR replaces the old report with a datavzrd one, updates rust-bio-tools version used (vcf-split behaviour changed such that the order of appearance of BND records in the VCF file is unchanged when split) and also now uses an official varlociraptor release (instead of a specific git revision on a branch that has since been merged+deleted).

[gpappasunb]

Problem with datavzrd report

Hello @tedil, I am getting the following error:

Error in rule datavzrd_circle_calls:
   jobid: 719
   output: results/datavzrd-report/all.fdr-controlled
   log: logs/datavzrd_report/all.log (check log file(s) for error message)

   shell:
       datavzrd resources/datavzrd/all.datavzrd.yaml --output results/datavzrd-report/all.fdr-controlled &> logs/datavzrd_report/all.log
       (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

The problem seems to be in the all.datavzrd.yaml config file:

datavzrd resources/datavzrd/all.datavzrd.yaml --output results/datavzrd-report/all.fdr-controlled
Error: views.circles-barcode01.render-table: unknown field `direction`, expected `columns` or `headers` at line 41 column 7

The generated template in the yaml file contains:

    dataset: barcode01-circles
    render-table:
      direction:
        display-mode: hidden
      regex('AF_(.+)'):
        plot:
          ticks:
            scale: linear
            domain:
            - 0.0
            - 1.0
            aux-domain-columns:
            - regex('AF_(.+)')

Sounds that headers and columns entries are missing.

Regards

[tedil]

Problem with datavzrd report

Hello @tedil, I am getting the following error:

Error in rule datavzrd_circle_calls:
   jobid: 719
   output: results/datavzrd-report/all.fdr-controlled
   log: logs/datavzrd_report/all.log (check log file(s) for error message)

   shell:
       datavzrd resources/datavzrd/all.datavzrd.yaml --output results/datavzrd-report/all.fdr-controlled &> logs/datavzrd_report/all.log
       (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

The problem seems to be in the all.datavzrd.yaml config file:

datavzrd resources/datavzrd/all.datavzrd.yaml --output results/datavzrd-report/all.fdr-controlled
Error: views.circles-barcode01.render-table: unknown field `direction`, expected `columns` or `headers` at line 41 column 7

The generated template in the yaml file contains:

    dataset: barcode01-circles
    render-table:
      direction:
        display-mode: hidden
      regex('AF_(.+)'):
        plot:
          ticks:
            scale: linear
            domain:
            - 0.0
            - 1.0
            aux-domain-columns:
            - regex('AF_(.+)')

Sounds that headers and columns entries are missing.

Regards

Thank you @gpappasunb for the report -- I think this may be a problem with the datavzrd version used (because some of the keywords changed between versions etc). Meanwhile --if you're feeling a little bit adventurous -- you might want to check out the better-tables branch, which produces a report which is structured better and is easier to navigate (and does not run into the problem you mentioned any more!)