Adding Illumina version of HIV-GC workflow

[frankambrosio3]

using the ivar version of the theiacov assembly process (with new scheme) implement a new workflow: hivgc_illumina

[frankambrosio3]

Modified versions of these files required for the new workflow:

• [ ] wf_read_qc_trim.wdl
• This workflow measures sc2 read percentage with Kraken, task and output should be removed

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• [x] task_alignment.wdl
• In the bwa task there is an optional input for ref, and if no ref is given, default ref will be the sars-cov-2 ref. Replace this with the hiv ref

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• [x] task_consensus_call.wdl
• Primer trimming task looks fine
• In variant_call min_depth default will need to be lowered
• Also in variant_call task, default reference assembly and gff must be swapped for HIV refs
• In consensus task, min_depth default value should also be lowered
• In consensus task, reference genome default must be swapped for HIV ref

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• [ ] task_assembly_metrics
• swap s gene coverage for pol region coverage

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• [x] task_taxon_id.wdl
• Quasitools task will need to be modified to accept paired end reads

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• [ ] task_ncbi.wdl
• Remove task from workflow

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• [x] task_qc_utils.wdl
• line 194, genome length should be HIV ref length

[frankambrosio3]

Left in ncbi for human read scrubbing (which is particularly important with HIV data. pol region coverage will need to be an addition in the a new version