adding viloca to the workflow

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[LaraFuhrmann]

Tested VILOCA on the hiv-tutorial data CAP188 4 using the following config files to test uniform-tiling strategy and amplicon tiling strategy.

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

viloca:
    consensus: false

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

viloca:
    consensus: false
    insert_bedfile: resources/samples/insert.bed

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false

[LaraFuhrmann]

Now we are adding the smallgenomeutilities scritp to merge the paried-end reads into one read. This is since viloca can then be applied to the merged reads with longer local regions / windows.

An example config file could look like this:

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

viloca:
    merge_paired_end_reads: true    
    consensus: false

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false

[LaraFuhrmann]

We are also adding the paired_end_read_merger from smallgenomeutilities to the workflow.

The workflow as tested with a ww SARS-CoV-2 sample using the following config file: (note we cheated by providing already an aligned bam file to V-pipe here, but the paired-end-read-merger and viloca were executed.)

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

applications:
    paired_end_read_merger: /Users/lfuhrmann/Downloads/smallgenomeutilities-dev/scripts/paired_end_read_merger

viloca:
    merge_paired_end_reads: true
    consensus: false

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false

There is a bug in the paired_end_read_merger as VILOCA is reporting ValueError: Soft clipping only possible on the edges of a read.

[LaraFuhrmann]

For completeness, VILOCA also runs when we don't choose to the read merging.

general:
    virus_base_config: ""
    aligner: bwa
    snv_caller: viloca

input:
    reference: "{VPIPE_BASEDIR}/../resources/hiv/HXB2.fasta"
    metainfo_file: "{VPIPE_BASEDIR}/../resources/hiv/metainfo.yaml"
    gff_directory: "{VPIPE_BASEDIR}/../resources/hiv/gffs/"
    # NOTE: this input datadir isn't standard
    datadir: resources/samples/
    read_length: 301
    samples_file: samples.tsv
    paired: true

applications:
    paired_end_read_merger: /Users/lfuhrmann/Downloads/smallgenomeutilities-dev/scripts/paired_end_read_merger

viloca:
    merge_paired_end_reads: false
    consensus: false

output:
    snv: true
    local: false
    global: false
    visualization: false
    QA: false