Add intermediate frequency mutations screen TheiaCoV

[michellescribner]

This PR:

• Modifies the variant_call task such that it calculates the proportion of variants at intermediate allele frequencies (60-90%). This value is reported in the output: ivar_variant_proportion_intermediate for workflows that use iVar to perform variant calling (TheiaCoV_Illumina_PE and TheiaCoV_Illumina_SE)

• These changes have been tested on ~700 paired-end SARS-CoV-2 samples and verified to yield the expected value based on the variants shown in the iVar tsv result file

• https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/dataAnalysis_SARS-CoV-2_CDPH_Master_clone_2021-08-24/job_history/13141b80-fe88-46ae-869c-1804f7c62a73

[sage-wright]

🌟

[kevinlibuit]

Approving as is for PHVG. Notes for potential updates as we migrate things to PHB:

• Capturing total variants and int variants integers could be valuable outputs, especially in instances where organism number of variants isn't as predictable as SC2

[kevinlibuit]

Approving as is for PHVG. Notes for potential updates as we migrate things to PHB:

• Capturing total variants and int variants integers could be valuable outputs, especially in instances where organism number of variants isn't as predictable as SC2

Especially for organisms that require different references