Multiqc

[LouisLeNezet]

Improve the output of multiqc and add more statistics.

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[atrigila]

Nice job. A question can the general statistics be split in sections for each of the major subworkflows? So that when the user browses the report they can see if the statistics are before/after imputation.

[LouisLeNezet]

Hi @atrigila !
I've tried to split by step using the following in the multiqc_config.yml.

run_modules:
    - "samtools"
    - "bcftools"

top_modules:
    - "samtools"
    - "bcftools":
        name: "BCFtools (original VCF)"
        info: "BCFtools stats of original files"
        path_filters:
            - "*.panel.bcftools_stats.txt"
            - "*.truth.bcftools_stats.txt"
    - "bcftools":
        name: "BCFtools (imputed VCF)"
        info: "BCFtools stats of imputed files"
        path_filters:
            - "*.glimpse1.bcftools_stats.txt"
            - "*.glimpse2.bcftools_stats.txt"
            - "*.stitch.bcftools_stats.txt"
            - "*.quilt.bcftools_stats.txt"

This does separate the section by step but the general statistic table is then messed up.

So for the moment I think it is preferable to keep everything together.
It also allows to easy compare the truth to the imputed files.