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Add support for variant scoring by MIVMIR, GICAM models #812
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| [Version] | ||
| version = 1 | ||
| name = rank_model_for_gicam | ||
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| [Categories] | ||
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| [[inheritance_models]] | ||
| category_aggregation = min | ||
|
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| [[variant_call_quality_filter]] | ||
| category_aggregation = sum | ||
|
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| [model_score] | ||
| category = variant_call_quality_filter | ||
| data_type = integer | ||
| description = Inheritance model score | ||
| field = INFO | ||
| info_key = ModelScore | ||
| record_rule = min | ||
| separators = ',',':', | ||
|
|
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| [[not_reported]] | ||
| score = 0 | ||
|
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| [[low_qual]] | ||
| score = -5 | ||
| lower = 0 | ||
| upper = 10 | ||
|
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| [[medium_qual]] | ||
| score = -2 | ||
| lower = 10 | ||
| upper = 20 | ||
|
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| [[high_qual]] | ||
| score = 0 | ||
| lower = 20 | ||
| upper = 300 | ||
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| [genetic_models] | ||
| category = inheritance_models | ||
| data_type = string | ||
| description = Inheritance models followed for the variant | ||
| field = INFO | ||
| info_key = GeneticModels | ||
| record_rule = max | ||
| separators = ',', ':', '|', | ||
|
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| [[ad]] | ||
| priority = 1 | ||
| score = 1 | ||
| string = 'AD' | ||
|
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||
| [[ad_dn]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'AD_dn' | ||
|
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| [[ar]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'AR_hom' | ||
|
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| [[ar_dn]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'AR_hom_dn' | ||
|
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| [[ar_comp]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'AR_comp' | ||
|
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| [[ar_comp_dn]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'AR_comp_dn' | ||
|
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| [[xr]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'XR' | ||
|
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| [[xr_dn]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'XR_dn' | ||
|
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| [[xd]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'XD' | ||
|
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| [[xd_dn]] | ||
| score = 1 | ||
| priority = 1 | ||
| string = 'XD_dn' | ||
|
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| [[not_reported]] | ||
| score = -12 | ||
|
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| [filter] | ||
| category = variant_call_quality_filter | ||
| data_type = string | ||
| description = The filters for the variant | ||
| field = FILTER | ||
| record_rule = min | ||
| separators = ';', | ||
|
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| [[not_reported]] | ||
| score = 0 | ||
|
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| [[pass]] | ||
| score = 3 | ||
| priority = 1 | ||
| string = 'PASS' | ||
|
|
||
| [[dot]] | ||
| score = 3 | ||
| priority = 2 | ||
| string = '.' |
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|
torbjorgen marked this conversation as resolved.
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| process GICAM_INFER { | ||
| // https://github.com/Clinical-Genomics/rdds/tree/master/src/rdds/gicam | ||
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| tag "${meta.id}" | ||
| label 'process_high' | ||
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| container "docker.io/clinicalgenomics/rdds_mivmir:v1.13.0" | ||
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| beforeScript "mkdir ${task.workDir}/rdds-tmp" | ||
| afterScript "rm -r ${task.workDir}/rdds-tmp" | ||
| containerOptions {[ | ||
| workflow.containerEngine.equals("singularity") ? "--bind ${task.workDir}/rdds-tmp:/rdds/tmp" : "", | ||
| workflow.containerEngine.equals("docker") ? "--tmpfs /rdds/tmp": "", | ||
| "" | ||
| ].minus("").join(" ")} | ||
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fellen31 marked this conversation as resolved.
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| input: | ||
| tuple val(meta), path(input_vcf) | ||
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| output: | ||
| tuple val(meta), path('*-predictions.vcf'), emit: vcf | ||
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torbjorgen marked this conversation as resolved.
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| tuple val("${task.process}"), val('gicam'), val('v1.13.0'), topic: versions, emit: versions_gicam | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| """ | ||
| . /opt/pyenv/bin/activate | ||
| export PYTHONPATH=/rdds/src | ||
| python3 -m rdds.gicam infer-vcf --cpu_cores ${task.cpus} ${input_vcf} | ||
| """ | ||
| } | ||
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