Joint Germline subworkflow haplotypecaller -> Vqsr #595
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| Original file line number | Diff line number | Diff line change | ||||
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@@ -606,9 +606,6 @@ process{ | |||||
| ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" } | ||||||
| ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1' | ||||||
| ext.when = { params.tools && params.tools.split(',').contains('freebayes') } | ||||||
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| } | ||||||
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| withName: 'BCFTOOLS_SORT' { | ||||||
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@@ -644,17 +641,13 @@ process{ | |||||
| ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) } | ||||||
| ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') } | ||||||
| publishDir = [ | ||||||
| enabled: !params.joint_germline, | ||||||
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| mode: params.publish_dir_mode, | ||||||
| path: { "${params.outdir}/variant_calling/"}, | ||||||
| pattern: "*{vcf.gz,vcf.gz.tbi}", | ||||||
| saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${meta.id}/${it}" } | ||||||
| ] | ||||||
| } | ||||||
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| withName: 'FILTERVARIANTTRANCHES' { | ||||||
| ext.prefix = {"${meta.id}.haplotypecaller"} | ||||||
| ext.args = { "--info-key CNN_1D" } | ||||||
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@@ -665,12 +658,48 @@ process{ | |||||
| ] | ||||||
| } | ||||||
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| withName: 'GATK4_GENOMICSDBIMPORT' { | ||||||
| ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name : "joint_interval" } | ||||||
| ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals} | ||||||
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| } | ||||||
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| withName: 'GATK4_GENOTYPEGVCFS' { | ||||||
| ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name: "joint_interval" } | ||||||
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There was a problem hiding this comment. we had There was a problem hiding this comment. And no more when statement for this one? There was a problem hiding this comment. either the merged and unmerged should have the same name so that regardless if 1 interval or a 100, the output file always has the same name |
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| } | ||||||
| withName: 'MERGE_GENOTYPEGVCFS' { | ||||||
| ext.prefix = "joint_germline" | ||||||
| publishDir = [ | ||||||
| mode: params.publish_dir_mode, | ||||||
| path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" }, | ||||||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||||||
| pattern: "*{vcf.gz,vcf.gz.tbi}" | ||||||
| ] | ||||||
| } | ||||||
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| withName: 'VARIANTRECALIBRATOR_INDEL' { | ||||||
| ext.prefix = { "${meta.id}_INDEL" } | ||||||
| ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL" | ||||||
| } | ||||||
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| withName: 'VARIANTRECALIBRATOR_SNP' { | ||||||
| ext.prefix = { "${meta.id}_SNP" } | ||||||
| ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP" | ||||||
| } | ||||||
| withName: 'GATK4_APPLYVQSR_SNP'{ | ||||||
| ext.prefix = { "${meta.id}_SNP" } | ||||||
| ext.args = '--truth-sensitivity-filter-level 99.9 -mode SNP' | ||||||
| } | ||||||
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| withName: 'GATK4_APPLYVQSR_INDEL'{ | ||||||
| ext.prefix = { "${meta.id}_INDEL" } | ||||||
| ext.args = '--truth-sensitivity-filter-level 99.9 -mode INDEL' | ||||||
| } | ||||||
| withName: 'MERGE_VQSR' { | ||||||
| ext.prefix = "joint_germline_recalibrated" | ||||||
| publishDir = [ | ||||||
| mode: params.publish_dir_mode, | ||||||
| path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"}, | ||||||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||||||
| pattern: "*{vcf.gz,vcf.gz.tbi}" | ||||||
| ] | ||||||
| } | ||||||
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| Original file line number | Diff line number | Diff line change |
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@@ -26,7 +26,6 @@ nextflow.enable.dsl = 2 | |
| GENOME PARAMETER VALUES | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
| params.ascat_alleles = WorkflowMain.getGenomeAttribute(params, 'ascat_alleles') | ||
| params.ascat_genome = WorkflowMain.getGenomeAttribute(params, 'ascat_genome') | ||
| params.ascat_loci = WorkflowMain.getGenomeAttribute(params, 'ascat_loci') | ||
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@@ -37,15 +36,20 @@ params.bwamem2 = WorkflowMain.getGenomeAttribute(params, 'bwamem2' | |
| params.chr_dir = WorkflowMain.getGenomeAttribute(params, 'chr_dir') | ||
| params.dbsnp = WorkflowMain.getGenomeAttribute(params, 'dbsnp') | ||
| params.dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'dbsnp_tbi') | ||
| params.dbsnp_vqsr = WorkflowMain.getGenomeAttribute(params, 'dbsnp_vqsr') | ||
| params.dict = WorkflowMain.getGenomeAttribute(params, 'dict') | ||
| params.dragmap = WorkflowMain.getGenomeAttribute(params, 'dragmap') | ||
| params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') | ||
| params.fasta_fai = WorkflowMain.getGenomeAttribute(params, 'fasta_fai') | ||
| params.germline_resource = WorkflowMain.getGenomeAttribute(params, 'germline_resource') | ||
| params.germline_resource_tbi = WorkflowMain.getGenomeAttribute(params, 'germline_resource_tbi') | ||
| params.intervals = WorkflowMain.getGenomeAttribute(params, 'intervals') | ||
| params.known_snps = WorkflowMain.getGenomeAttribute(params, 'known_snps') | ||
| params.known_snps_tbi = WorkflowMain.getGenomeAttribute(params, 'known_snps_tbi') | ||
| params.known_snps_vqsr = WorkflowMain.getGenomeAttribute(params, 'known_snps_vqsr') | ||
| params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels') | ||
| params.known_indels_tbi = WorkflowMain.getGenomeAttribute(params, 'known_indels_tbi') | ||
| params.known_indels_vqsr = WorkflowMain.getGenomeAttribute(params, 'known_indels_vqsr') | ||
| params.mappability = WorkflowMain.getGenomeAttribute(params, 'mappability') | ||
| params.pon = WorkflowMain.getGenomeAttribute(params, 'pon') | ||
| params.pon_tbi = WorkflowMain.getGenomeAttribute(params, 'pon_tbi') | ||
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@@ -160,7 +160,7 @@ | |
| "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7" | ||
| }, | ||
| "gatk4/variantrecalibrator": { | ||
| "git_sha": "edfe28a5e0088b66ee92e7c58186059f9b5e62d5" | ||
| }, | ||
| "manta/germline": { | ||
| "git_sha": "ffedf09b6e84b479c9c901274f74bb33f3777243" | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -64,6 +64,7 @@ params { | |
| cf_window = null // by default we are not using this in Control-FREEC | ||
| ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2 | ||
| wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers | ||
| joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected | ||
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| // Annotation | ||
| vep_out_format = 'vcf' | ||
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@@ -232,6 +232,12 @@ | |
| "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools.", | ||
| "help_text": "This can speed up computation for somatic variant calling with matched normal samples. If false, all normal samples are processed as well through the germline variantcalling tools. If true, only somatic variant calling is done." | ||
| }, | ||
| "joint_germline": { | ||
| "type": "boolean", | ||
| "fa_icon": "fas fa-toolbox", | ||
| "description": "Turn on the joint germline variant calling for GATK haplotypecaller", | ||
| "help_text": "Uses all normal germline samples (as designated by `status` in the input csv) in the joint germline variant calling process." | ||
| }, | ||
| "ascat_min_base_qual": { | ||
| "type": "number", | ||
| "default": 20, | ||
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@@ -554,6 +560,11 @@ | |
| "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\n> **NB** If none provided, will be generated automatically from the dbsnp file. Combine with `--save_reference` to save for future runs.", | ||
| "hidden": true | ||
| }, | ||
| "dbsnp_vqsr": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-copy", | ||
| "description": "label string for VariantRecalibration (haplotypecaller joint variant calling)" | ||
| }, | ||
| "dict": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-file", | ||
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@@ -611,6 +622,27 @@ | |
| "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\n> **NB** If none provided, will be generated automatically from the known index file, if provided. Combine with `--save_reference` to save for future runs.", | ||
| "hidden": true | ||
| }, | ||
| "known_indels_vqsr": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-copy", | ||
| "description": "1st label string for VariantRecalibration (haplotypecaller joint variant calling)" | ||
| }, | ||
| "known_snps": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-copy", | ||
| "description": "Path to known snps file." | ||
| }, | ||
| "known_snps_tbi": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-copy", | ||
| "description": "Path to known snps file snps.", | ||
| "help_text": "> **NB** If none provided, will be generated automatically from the known index file, if provided. Combine with `--save_reference` to save for future runs." | ||
| }, | ||
| "known_snps_vqsr": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-copy", | ||
| "description": "label string for VariantRecalibration (haplotypecaller joint variant calling)" | ||
| }, | ||
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| "mappability": { | ||
| "type": "string", | ||
| "fa_icon": "fas fa-file", | ||
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The files are not yet on igenomes, so I would update this all together in #662 once they are there