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Filter SNVs, INDELs, CNVs and SVs (#496)
* Filter variants * CHANGELOG * Update CHANGELOG.md * Update assets/schema_hgnc_ids.json * Update subworkflows/local/filter_variants/main.nf Co-authored-by: Daniel Schmitz <[email protected]> * merge and review suggestions * review suggestions * Update subworkflows/local/filter_variants/main.nf Co-authored-by: Anders Jemt <[email protected]> * Review suggestions --------- Co-authored-by: Daniel Schmitz <[email protected]> Co-authored-by: Anders Jemt <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_hgnc_ids.json", | ||
| "title": "genomic-medicine-sweden/nallo pipeline - params.filter_variants_hgnc_ids schema", | ||
| "description": "Schema for the file provided with params.filter_variants_hgnc_ids", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "hgnc_id": { | ||
| "oneOf": [ | ||
| { | ||
| "type": "string", | ||
| "pattern": "^\\S+$" | ||
| }, | ||
| { | ||
| "type": "integer" | ||
| } | ||
| ], | ||
| "exists": true, | ||
| "errorMessage": "HGNC IDs must exist with a header line `hgnc_id`, then one HGNC ID per line, either as e.g. `4826` or `HGNC:4826`." | ||
| } | ||
| }, | ||
| "required": ["hgnc_id"] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
|
|
||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Filter variants | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
|
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||
| withName: '.*:FILTER_VARIANTS_SNV:.*' { | ||
| publishDir = [ | ||
| enabled: false, | ||
| ] | ||
| } | ||
|
|
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| withName: '.*:FILTER_VARIANTS_SNVS:ENSEMBLVEP_FILTERVEP' { | ||
| ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } | ||
| publishDir = [ | ||
| enabled: false, | ||
| ] | ||
| } | ||
|
|
||
| withName: '.*:FILTER_VARIANTS_SVS:ENSEMBLVEP_FILTERVEP' { | ||
| ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } | ||
| publishDir = [ | ||
| enabled: false, | ||
| ] | ||
| } | ||
|
|
||
| withName: '.*:FILTER_VARIANTS_SNVS:BCFTOOLS_VIEW' { | ||
| ext.prefix = { params.skip_snv_annotation ? "${meta.id}_snvs_filtered" : (params.skip_rank_variants ? "${meta.id}_snvs_annotated_filtered" : "${meta.id}_snvs_annotated_ranked_filtered") } | ||
| ext.args = { [ | ||
| '--output-type z', | ||
| '--write-index=tbi', | ||
| "${params.filter_snvs_expression}" | ||
| ].join(" ") } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/snvs/multi_sample/${meta.id}" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
|
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| withName: '.*:FILTER_VARIANTS_SVS:BCFTOOLS_VIEW' { | ||
| ext.prefix = { | ||
| def parts = [] | ||
| parts << "${meta.id}" | ||
| parts << (params.skip_cnv_calling ? 'svs_merged' : 'svs_cnvs_merged') | ||
| if (!params.skip_sv_annotation) parts << 'annotated' | ||
| if (!params.skip_rank_variants) parts << 'ranked' | ||
| parts << 'filtered' | ||
| return parts.join('_') | ||
| } | ||
| ext.args = { [ | ||
| '--output-type z', | ||
| '--write-index=tbi', | ||
| "${params.filter_svs_expression}" | ||
| ].join(" ") } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/svs/family/${meta.id}" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
|
||
| } |
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