DI-601 v1.4.0 Variant counts and multiple reports per sample

Changes

Adds number of samples released in the links file
Adds SNV/CNV counts and clinical indication in Excel report if available
- If counts available, removes SNV or CNV report download URLs if no SNVs pass filtering/no CNVs detected
Allows releasing of multiple SNV and CNV reports per sample (i.e. if reports are split by clinical indication because Dias batch was run with -isplit_tests=true)
- Orders SNV and CNV reports by panel (if present)
- Names CNV IGV session files using part of CNV report name so they are named differently if multiple session files are made for the same sample
Adds optional input -ilock_cells which locks any Excel cells which are populated from editing (default True)
Adds optional input -imultiqc_report of MultiQC report file (closes #18)
Updates README to include the correct default URL duration (closes #17)
Fixes typo in dxapp.json (closes #15)

Example test jobs New format Excel report metadata (clinical indications and variant counts) present, reports split per sample by panel, cells locked, MultiQC report given as input. One sample (line 586) is split into multiple reports. Job: https://platform.dnanexus.com/panx/projects/Gf1JZfQ4FBj30ZjFQjKp3FQ3/data/?scope=project&id.values=file-GfPGxJ84FBjFB9P06Qf0q1F9

As current set up No Excel report metadata (counts or clinical indications) present for these reports so no clinical indications or counts present or links removed in final Excel. Reports aren't split by clinical indication so only a single report given back per sample. Excel cells not locked for editing Job: https://platform.dnanexus.com/panx/projects/Gf1JZfQ4FBj30ZjFQjKp3FQ3/monitor/job/GfPv29Q4FBjFb5y3ykXk7P08

This change is

eastgenomics / eggd_artemis