Dataops 906 multiqc updates

[kjellinjonas]

MultiQC updates:

removed multiqc_config_wgs_qc.yaml

• Not used anymore

updated multiqc_config_wgs.yaml

• removed plot (mosdepth-coverage-per-contig) since it was ugly and not informative
• Updated formatting of General stats table
  • made >=10X coverage column visible
  • made irrelevant stats invisible
  • Grouped samples

updated multiqc_pipeline_info.py

• Corrected input file so it is compatible with new sarek
• Updated regex to work with the new input file

updated sample_list_for_multiqc.py

• Changed identifier string for Sarek sample sheet
• Made it compatible with new samplesheet format
  • Changed delimiter
  • Added step to skip header of samplesheet

updated multiqc_sarek_project.sh

• Now requires project ID to be given in the command line to make it more flexible.
  Before the project ID was parsed from the input path which is not ideal when running
  multiqc from a non-canonical path e.g. FU projects.
  multiqc_sarek_project $PWD
• Now calls multiqc_extra_stats_qc.py
• Creates a new folder and moves the output from multiqc_extra_stats_qc.py there.
  If these files would be moved to the multiqc_custom_content folder, as the other custom files, the QC check would be included in the user report as well.
• Changed paths to be compatible with new sarek output folder structure
• Updated MultiQC call to reference the new files

new script multiqc_extra_stats_qc.py

• Calculates Autosomal coverage, GC % and % mapped reads
• Parse precalculated values for 10/30 X coverage, Unfiltered variants and Average insert size
• Performs QC check according to INS-00123
• Values in QC class should be updated if INS-00123 is updated
• Output a yaml file with data to be added to MultiQC General stats
• Output a yaml file which will create a QC section in MultiQC report

[matrulda]

Excellent work, I left some comments for you.

[matrulda]

Something happened with the indentation here.

[matrulda]

Looks good! Just something weird with the indentation on one line.