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Merged
nourmahfel merged 2 commits into from
Mar 20, 2026
Merged

Final update #29

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5f52a11
Final update
nourmahfel Mar 19, 2026
ff6e869
Final update
nourmahfel Mar 19, 2026
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6 changes: 3 additions & 3 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -649,7 +649,7 @@ process {
}

withName: 'STRANGER' {
ext.prefix = { "${meta.id}_annotated_vcf" }
ext.prefix = { "${meta.id}_annotated" }
publishDir = [
path: { "${params.outdir}/${meta.id}/str" },
mode: 'copy'
Expand All @@ -667,7 +667,7 @@ process {


withName: 'ANNOTSV_SNIFFLES' {
ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38 -rankFiltering '3-5,NA'" }
ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
ext.prefix = { "${meta.id}_annotsv" }
containerOptions = '--user root'
publishDir = [
Expand All @@ -677,7 +677,7 @@ process {
}

withName: 'ANNOTSV_SVIM' {
ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38 -rankFiltering '3-5,NA'" }
ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" }
ext.prefix = { "${meta.id}_annotsv" }
containerOptions = '--user root'
publishDir = [
Expand Down
4 changes: 2 additions & 2 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,11 @@ params {
// ========================================
sniffles_min_mapq = 10
annotate_sv = true
rankfiltering = '3-5,NA'
rankfiltering = '1-5,NA'
run_svim = true
svim_min_mapq = 10
filter_pass_sv = true
downsample_sv = true
downsample_sv = false
coverage_bed = null
min_read_support = 'auto'
min_read_support_limit = 2
Expand Down
4 changes: 2 additions & 2 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@
},
"rankfiltering": {
"type": "string",
"default": "3-5,NA",
"default": "1-5,NA",
"title": "Rank Filtering",
"description": "Rank filtering criteria"
},
Expand Down Expand Up @@ -265,7 +265,7 @@
},
"downsample_sv": {
"type": "boolean",
"default": true,
"default": false,
"description": "Enable SV filtering by coverage.",
"fa_icon": "fas fa-filter"
},
Expand Down
23 changes: 19 additions & 4 deletions subworkflows/local/annotate_sv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@ workflow ANNOTATE_SV {

take:
ch_samplesheet
ch_sv_vcf
ch_sniffles_vcf
ch_svim_vcf
ch_snv_vcf
candidate_genes
false_positive_snv
Expand Down Expand Up @@ -38,7 +39,7 @@ workflow ANNOTATE_SV {
ch_false_positive_snv = false_positive_snv ? Channel.fromPath(false_positive_snv).map{[[id:"false_positive"], it]}.collect() : Channel.value([[id:"empty"], []])
ch_gene_transcripts = gene_transcripts ? Channel.fromPath(gene_transcripts).map{[[id:"transcripts"], it]}.collect() : Channel.value([[id:"empty"], []])

ch_annotate_input = ch_sv_vcf
ch_annotate_input_sniffles = ch_sniffles_vcf
.map { meta, vcf -> [meta.id, meta, vcf] }
.join(
ch_samplesheet.map { meta, data -> [meta.id, data.hpo_terms] },
Expand All @@ -54,15 +55,29 @@ workflow ANNOTATE_SV {
}

ANNOTSV_SNIFFLES (
ch_annotate_input,
ch_annotate_input_sniffles,
ch_annotsv_annotations,
ch_candidate_genes,
ch_false_positive_snv,
ch_gene_transcripts
)

if (params.run_svim){
ANNOTSV_SVIM (ch_annotate_input,
ch_annotate_input_svim = ch_svim_vcf
.map { meta, vcf -> [meta.id, meta, vcf] }
.join(
ch_samplesheet.map { meta, data -> [meta.id, data.hpo_terms] },
by: 0
)
.join(
ch_snv_vcf.map { meta, vcf -> [meta.id, vcf] },
by: 0
)
.map { id, meta, sv_vcf, hpo, snv_vcf ->
def clean_hpo = (hpo && hpo.trim()) ? hpo : null
[meta + [hpo_terms: clean_hpo], sv_vcf, [], snv_vcf]
}
ANNOTSV_SVIM (ch_annotate_input_svim,
ch_annotsv_annotations,
ch_candidate_genes,
ch_false_positive_snv,
Expand Down
72 changes: 48 additions & 24 deletions subworkflows/local/annotate_sv/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -26,26 +26,32 @@ nextflow_workflow {
[ hpo_terms: 'HP:0001250;HP:0000252' ]
])

// ch_sv_vcf - [meta, vcf]
// ch_sniffles_vcf - [meta, vcf]
input[1] = Channel.of([
[ id:'test_sample' ],
file('test_sniffles.vcf')
])

// ch_snv_vcf - [meta, vcf]
// ch_svim_vcf - [meta, vcf]
input[2] = Channel.of([
[ id:'test_sample' ],
file('test_svim.vcf')
])

// ch_snv_vcf - [meta, vcf]
input[3] = Channel.of([
[ id:'test_sample' ],
file('test_snv.vcf')
])

// candidate_genes - path or null
input[3] = null
input[4] = null

// false_positive_snv - path or null
input[4] = null
input[5] = null

// gene_transcripts - path or null
input[5] = null
input[6] = null
"""
}
}
Expand Down Expand Up @@ -76,26 +82,32 @@ nextflow_workflow {
[ hpo_terms: 'HP:0001250;HP:0000252' ]
])

// ch_sv_vcf
// ch_sniffles_vcf
input[1] = Channel.of([
[ id:'test_sample' ],
file('test_sniffles.vcf')
])

// ch_snv_vcf
// ch_svim_vcf
input[2] = Channel.of([
[ id:'test_sample' ],
file('test_svim.vcf')
])

// ch_snv_vcf
input[3] = Channel.of([
[ id:'test_sample' ],
file('test_snv.vcf')
])

// candidate_genes
input[3] = 'candidate_genes.txt'
input[4] = 'candidate_genes.txt'

// false_positive_snv
input[4] = 'false_positive_snv.txt'
input[5] = 'false_positive_snv.txt'

// gene_transcripts
input[5] = 'gene_transcripts.txt'
input[6] = 'gene_transcripts.txt'
"""
}
}
Expand All @@ -120,32 +132,38 @@ nextflow_workflow {
}
workflow {
"""
// ch_samplesheet - empty hpo_terms
// ch_samplesheet
input[0] = Channel.of([
[ id:'test_sample' ],
[ hpo_terms: '' ]
[ hpo_terms: 'HP:0001250;HP:0000252' ]
])

// ch_sv_vcf
// ch_sniffles_vcf
input[1] = Channel.of([
[ id:'test_sample' ],
file('test_sniffles.vcf')
])

// ch_snv_vcf
// ch_svim_vcf
input[2] = Channel.of([
[ id:'test_sample' ],
file('test_svim.vcf')
])

// ch_snv_vcf
input[3] = Channel.of([
[ id:'test_sample' ],
file('test_snv.vcf')
])

// candidate_genes
input[3] = null
input[4] = 'candidate_genes.txt'

// false_positive_snv
input[4] = null
input[5] = 'false_positive_snv.txt'

// gene_transcripts
input[5] = null
input[6] = 'gene_transcripts.txt'
"""
}
}
Expand All @@ -169,32 +187,38 @@ nextflow_workflow {
}
workflow {
"""
// ch_samplesheet - null hpo_terms
// ch_samplesheet
input[0] = Channel.of([
[ id:'test_sample' ],
[ hpo_terms: null ]
[ hpo_terms: 'HP:0001250;HP:0000252' ]
])

// ch_sv_vcf
// ch_sniffles_vcf
input[1] = Channel.of([
[ id:'test_sample' ],
file('test_sniffles.vcf')
])

// ch_snv_vcf
// ch_svim_vcf
input[2] = Channel.of([
[ id:'test_sample' ],
file('test_svim.vcf')
])

// ch_snv_vcf
input[3] = Channel.of([
[ id:'test_sample' ],
file('test_snv.vcf')
])

// candidate_genes
input[3] = null
input[4] = 'candidate_genes.txt'

// false_positive_snv
input[4] = null
input[5] = 'false_positive_snv.txt'

// gene_transcripts
input[5] = null
input[6] = 'gene_transcripts.txt'
"""
}
}
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/call_str/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
{
"id": "test_nanopore"
},
"test_nanopore_annotated_vcf.vcf.gz"
"test_nanopore_annotated.vcf.gz"
]
]
],
Expand All @@ -25,7 +25,7 @@
{
"id": "test_nanopore"
},
"test_nanopore_annotated_vcf.vcf.gz"
"test_nanopore_annotated.vcf.gz"
]
]
],
Expand Down
3 changes: 3 additions & 0 deletions workflows/longraredisease.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -552,6 +552,7 @@ workflow LONGRAREDISEASE {
)

ch_sv_vcf_final = CALL_SV.out.sniffles_vcf
ch_svim_vcf = CALL_SV.out.svim_vcf
ch_versions = ch_versions.mix(CALL_SV.out.versions)

if (params.filter_pass_sv) {
Expand Down Expand Up @@ -590,6 +591,7 @@ workflow LONGRAREDISEASE {
ch_svim_vcf = FILTER_SV_SVIM.out.ch_vcf_tbi.map { meta, vcf, tbi -> [meta, vcf] }

}

}

else {
Expand All @@ -606,6 +608,7 @@ workflow LONGRAREDISEASE {

ANNOTATE_SV(ch_samplesheet,
ch_sv_vcf_final,
ch_svim_vcf,
ch_snv_vcf,
[],
[],
Expand Down
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