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Update dnascope-module #422

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merged 4 commits into from
Sep 7, 2023
Merged

Update dnascope-module #422

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13eab83
Updating sentieon-dnascope module. Replacing parameter pcr_amplificat…
asp8200 Sep 5, 2023
15df0c0
Merge branch 'dev' into update_dnascope
asp8200 Sep 5, 2023
2a548e9
Update subworkflows/local/call_snv.nf
asp8200 Sep 7, 2023
e867829
Update subworkflows/local/variant_calling/call_snv_sentieon.nf
asp8200 Sep 7, 2023
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2 changes: 1 addition & 1 deletion conf/modules/annotate_snvs.config
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Expand Up @@ -66,7 +66,7 @@ process {
withName: '.*ANNOTATE_SNVS:CHROMOGRAPH_REGIONS' {
ext.prefix = { "${meta6.id}_rohann_vcfanno_upd_regions_chromograph" }
ext.args = { '--euploid' }
ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun }
tag = {"${meta6.id}"}
publishDir = [
path: { "${params.outdir}/annotate_snv" },
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7 changes: 3 additions & 4 deletions conf/modules/call_snv_sentieon.config
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Expand Up @@ -23,10 +23,9 @@ process {

withName: '.*CALL_SNV:CALL_SNV_SENTIEON:SENTIEON_DNASCOPE' {
ext.prefix = { "${meta.id}_dnascope" }
ext.args2 = { [
params.variant_type ? "--var_type ${params.variant_type}" : '',
params.pcr_amplification ? '' : "--pcr_indel_model NONE"
].join(" ") }
ext.args2 = {
params.variant_type ? "--var_type ${params.variant_type}" : ''
}
}

withName: '.*CALL_SNV:CALL_SNV_SENTIEON:SENTIEON_DNAMODELAPPLY' {
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2 changes: 1 addition & 1 deletion conf/modules/peddy_check.config
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Expand Up @@ -18,7 +18,7 @@
process {
withName: '.*:PEDDY_CHECK:PEDDY' {
// Peddy needs a bigger test set in order to run so we skip it for the two test profiles
ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun }
ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun }
publishDir = [
path: { "${params.outdir}/peddy_check" },
mode: params.publish_dir_mode,
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -377,7 +377,7 @@
},
"sentieon/dnascope": {
"branch": "master",
"git_sha": "127edadc279e19da093fdd513926c6cdee82c306",
"git_sha": "4fb6fdc8046ec09cd30f92a2a252e9a0ba4a6309",
"installed_by": ["modules"]
},
"sentieon/readwriter": {
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59 changes: 34 additions & 25 deletions modules/nf-core/sentieon/dnascope/main.nf
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94 changes: 55 additions & 39 deletions modules/nf-core/sentieon/dnascope/meta.yml
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12 changes: 6 additions & 6 deletions nextflow.config
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Expand Up @@ -44,14 +44,14 @@ params {
ml_model = ''

// Dnascope SNV calling
pcr_amplification = false
variant_type = 'snp,indel'
sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE'
variant_type = 'snp,indel'

// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null

// Boilerplate options
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11 changes: 7 additions & 4 deletions nextflow_schema.json
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Expand Up @@ -442,10 +442,13 @@
"fa_icon": "fas fa-align-center",
"description": "Interval in the reference that will be used in the software"
},
"pcr_amplification": {
"type": "boolean",
"description": "Indicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.",
"fa_icon": "fas fa-toggle-on"
"sentieon_dnascope_pcr_indel_model": {
"type": "string",
"default": "CONSERVATIVE",
"fa_icon": "fas fa-bacon",
"description": "Option for selecting the PCR indel model used by Sentieon Dnascope.",
"help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.",
"pattern": "^(NONE|HOSTILE|AGGRESSIVE|CONSERVATIVE)(?<!,)$"
},
"variant_caller": {
"type": "string",
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6 changes: 4 additions & 2 deletions subworkflows/local/call_snv.nf
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Expand Up @@ -9,14 +9,15 @@ include { GATK4_SELECTVARIANTS } from '../../modules/nf-core/gatk4/selectvariant

workflow CALL_SNV {
take:
ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ]
ch_known_dbsnp // channel: [optional] [ val(meta), path(vcf) ]
ch_known_dbsnp_tbi // channel: [optional] [ val(meta), path(tbi) ]
ch_call_interval // channel: [mandatory] [ path(intervals) ]
ch_ml_model // channel: [mandatory] [ path(model) ]
ch_case_info // channel: [mandatory] [ val(case_info) ]
ch_pcr_indel_model // channel: [mandatory] [ val(sentieon_dnascope_pcr_indel_model) ]
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main:
ch_versions = Channel.empty()
Expand All @@ -38,7 +39,8 @@ workflow CALL_SNV {
ch_known_dbsnp_tbi,
ch_call_interval,
ch_ml_model,
ch_case_info
ch_case_info,
ch_pcr_indel_model
)

ch_vcf = Channel.empty().mix(CALL_SNV_DEEPVARIANT.out.vcf, CALL_SNV_SENTIEON.out.vcf)
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37 changes: 26 additions & 11 deletions subworkflows/local/variant_calling/call_snv_sentieon.nf
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Expand Up @@ -14,21 +14,36 @@ include { BCFTOOLS_FILTER as BCF_FILTER_TWO } from '../../../modules/nf-c

workflow CALL_SNV_SENTIEON {
take:
ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ]
ch_dbsnp // channel: [mandatory] [ val(meta), path(vcf) ]
ch_dbsnp_index // channel: [mandatory] [ val(meta), path(tbi) ]
ch_call_interval // channel: [mandatory] [ val(meta), path(interval) ]
ch_ml_model // channel: [mandatory] [ val(meta), path(model) ]
ch_case_info // channel: [mandatory] [ val(case_info) ]

ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ]
ch_dbsnp // channel: [mandatory] [ val(meta), path(vcf) ]
ch_dbsnp_index // channel: [mandatory] [ val(meta), path(tbi) ]
ch_call_interval // channel: [mandatory] [ val(meta), path(interval) ]
ch_ml_model // channel: [mandatory] [ val(meta), path(model) ]
ch_case_info // channel: [mandatory] [ val(case_info) ]
ch_pcr_indel_model // channel: [mandatory] [ val(sentieon_dnascope_pcr_indel_model) ]
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main:
ch_versions = Channel.empty()

SENTIEON_DNASCOPE ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_dbsnp, ch_dbsnp_index, ch_call_interval, ch_ml_model )
// Combine bam and intervals
bam_bai_intervals = ch_bam_bai.combine(ch_call_interval)
.map{
meta, bam, bai, meta2, interval -> [meta, bam, bai, interval]
}

ch_dnamodelapply_in = SENTIEON_DNASCOPE.out.vcf.join(SENTIEON_DNASCOPE.out.index)
SENTIEON_DNASCOPE(
bam_bai_intervals,
ch_genome_fasta,
ch_genome_fai,
ch_dbsnp,
ch_dbsnp_index,
ch_ml_model,
ch_pcr_indel_model,
'VARIANT',
false)

ch_dnamodelapply_in = SENTIEON_DNASCOPE.out.vcf.join(SENTIEON_DNASCOPE.out.vcf_tbi)

SENTIEON_DNAMODELAPPLY ( ch_dnamodelapply_in, ch_genome_fasta, ch_genome_fai, ch_ml_model )

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3 changes: 2 additions & 1 deletion workflows/raredisease.nf
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Expand Up @@ -360,7 +360,8 @@ workflow RAREDISEASE {
ch_dbsnp_tbi,
ch_call_interval,
ch_ml_model,
ch_case_info
ch_case_info,
Channel.value(params.sentieon_dnascope_pcr_indel_model)
)
ch_versions = ch_versions.mix(CALL_SNV.out.versions)

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