Feature/multiqc

[anoronh4]

Addressing #807

This PR combines results from each sample/pair/cohort into a multiqc report for each level.
Sample Report includes alfred, fastp, hsmetrics for each sample.
Example juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_withsamplemod_frombammapping/bams/DU874146-T/multiqc/multiqc_report.html

Somatic Report includes conpair results for each pair.
Example /juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_withsamplemod_frombammapping/somatic/DU874145-T__DU874145-N/multiqc/multiqc_report.html

Cohort Report includes alfred, fastp, hsmetrics, conpair for each sample/pair in the cohort
Example /juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_withsamplemod_frombammapping/cohort_level/default_cohort/multiqc_report.html

Although there is some text highlighting for values that indicate poor quality (green, yellow and red for pass, warn and fail), further discussion might be needed to continue shaping pass/fail metrics and what metrics are displayed. Alfred shows many metrics but so far i have only added mapping quality as proof of concept, as we may be focused on only a few of the alfred categories.

Additional notes
A few variables were set as global even though they should have been set as local. We caught this while testing multiqc and as such have made the correction in the commit 803e345

[anoronh4]

Updated example files:
Cohort report
/juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_biggersamples/cohort_level/default_cohort/multiqc_report.html
Sample Report
/juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_biggersamples/bams/BRCA_03936-N/multiqc/multiqc_report.html
Somatic Report
/juno/work/ccs/noronhaa/tempo_multiqc/testmultiqc_noronhaa/results_biggersamples/somatic/BRCA_00423-T__BRCA_00423-N/multiqc/multiqc_report.html

Future directions:

• There are some helpful functions available in multiqc 1.9 but I found some bugs in the v1.9 singularity image that I'm working to address: docker image of multiqc:1.9 error with singularity  MultiQC/MultiQC#1221 (comment)
• Add WGS configurations as well and handle params.assayType == 'genome' (CollectHsMetrics not run)
• Add PASS/FAIL metrics to each each sample. This will require running the multiqc report as normal, then parsing the resulting general statistics table and annotating based on cutoffs, then running multiqc a second time with a file containing one column of PASS/FAIL/WARN

[gongyixiao]

In Alfred Mapping Quality, maybe it's good to show the percentage of reads instead of the read count. The advantage of showing percentage will be more obvious in the cohort report.

@gongyixiao This can be done easily. I wonder what else we should display from the Alfred report. A couple of examples include:

# Alignment summary metrics (ME).
# Read length distribution (RL).
# Mean base quality (BQ).
# Base content (BC).
# Mapping quality histogram (MQ).
# Coverage histogram (CO).
# Chromosome mapping statistics (CM).
# Insert size histogram (IS).
# InDel context (IC).
# InDel size (IZ).
# Chromosome GC-content (CG).
# GC-content (GC).
# Avg. target coverage (TC).
# On target rate (OT).

The alfred file is not automatically parsed by multiqc so we have to write the code to parse it.

These info might be able to obtain from qualimap (http://qualimap.bioinfo.cipf.es/). Exploring it here: #166

The idea is since qualimap is a built-in supported tool for multiQC, so we would like to use it for the information it can get to avoid building custom support for Alfred in multiQC. Only use Alfred and build custom support for it for Alfred specific metrics, like read group aware/ignore mapping quality statistics.

[gongyixiao]

A few more misc changes:

• fixed finding pre_multiqc_data
• fixed incorrect “warn” status
• fixed resource, 1.GB * task.attempt -> 3.GB * task.attempt
• removed title on the sidebar that was getting cut off
• i believe i addressed the problem of not finding .MQ.alfred.tsv