8000 Add parameters to skip snv calling and repeat analysis by ramprasadn · Pull Request #571 · nf-core/raredisease · GitHub
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Add parameters to skip snv calling and repeat analysis #571

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Merged
merged 9 commits into from
Jun 24, 2024
Merged

Add parameters to skip snv calling and repeat analysis #571

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306d03b
skip repeat analysis
ramprasadn Jun 20, 2024
74087e2
add skip_snv_calling
ramprasadn Jun 20, 2024
a27392d
add to nextflow.config
ramprasadn Jun 21, 2024
e39c099
reorder
ramprasadn Jun 21, 2024
ee2a11d
fix indents
ramprasadn Jun 21, 2024
a8e86f5
Merge branch 'patch' into modularize-everything-1
ramprasadn Jun 24, 2024
1043128
Merge branch 'dev' of github.com:nf-core/raredisease into modularize-…
ramprasadn Jun 24, 2024
db74304
update changelog
ramprasadn Jun 24, 2024
07ff9d3
review suggestions
ramprasadn Jun 24, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- Two new parameters `skip_snv_calling` and `skip_repeat_analysis` to skip snv calling and repeat analysis respectively [#571](https://github.com/nf-core/raredisease/pull/571)
- Two new parameters `mbuffer_mem` and `samtools_sort_threads` to control resources given to mbuffer and samtools sort in the bwameme module [#570](https://github.com/nf-core/raredisease/pull/570)

### `Changed`
Expand All @@ -24,6 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| ------------- | --------------------- |
| | mbuffer_mem |
| | samtools_sort_threads |
| | skip_repeat_analysis |
| | skip_snv_calling |

## 2.1.0 - Obelix [2024-05-29]

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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -38,10 +38,10 @@ params {
skip_me_annotation = false
skip_mt_annotation = false
skip_qualimap = false
skip_repeat_analysis = false
skip_snv_annotation = false
skip_snv_calling = false
skip_sv_annotation = false
skip_me_annotation = false
skip_mt_annotation = false
skip_mt_subsample = false
skip_vcf2cytosure = true
skip_vep_filter = false
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10 changes: 10 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -568,11 +568,21 @@
"description": "Specifies whether or not to subsample mt alignment.",
"fa_icon": "fas fa-toggle-on"
},
"skip_repeat_analysis": {
"type": "boolean",
"description": "Specifies whether or not to skip calling and annotation of repeat expansions.",
"fa_icon": "fas fa-toggle-on"
},
"skip_snv_annotation": {
"type": "boolean",
"description": "Specifies whether or not to skip annotate SNV subworkflow.",
"fa_icon": "fas fa-toggle-on"
},
"skip_snv_calling": {
"type": "boolean",
"description": "Specifies whether or not to skip nuclear and mitochondrial SNV calling and annotation.",
"fa_icon": "fas fa-toggle-on"
},
"skip_sv_annotation": {
"type": "boolean",
"description": "Specifies whether or not to skip annotate structural variant subworkflow.",
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288 changes: 156 additions & 132 deletions workflows/raredisease.nf
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Expand Up @@ -23,7 +23,6 @@ def mandatoryParams = [
"intervals_wgs",
"intervals_y",
"platform",
"variant_catalog",
"variant_caller"
]
def missingParamsCount = 0
Expand All @@ -32,6 +31,14 @@ if (params.run_rtgvcfeval) {
mandatoryParams += ["rtg_truthvcfs"]
}

if (!params.skip_repeat_analysis) {
mandatoryParams += ["variant_catalog"]
}

if (!params.skip_snv_calling) {
mandatoryParams += ["genome"]
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genome is also used by smncopynumbercaller, but maybe you're adding that in a later PR :)

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Yupe! I have a couple more PR's in line to be merged after this :D

}

if (!params.skip_snv_annotation) {
mandatoryParams += ["genome", "vcfanno_resources", "vcfanno_toml", "vep_cache", "vep_cache_version",
"gnomad_af", "score_config_snv", "variant_consequences_snv"]
Expand Down Expand Up @@ -355,9 +362,12 @@ workflow RAREDISEASE {

ch_scatter_split_intervals = ch_scatter.split_intervals ?: Channel.empty()

//
// ALIGNING READS, FETCH STATS, AND MERGE.
//
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ALIGN & FETCH STATS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

ALIGN (
ch_samplesheet,
ch_genome_fasta,
Expand Down Expand Up @@ -406,10 +416,13 @@ workflow RAREDISEASE {
)
ch_versions = ch_versions.mix(QC_BAM.out.versions)

//
// EXPANSIONHUNTER AND STRANGER
//
if (params.analysis_type.equals("wgs")) {
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CALL AND ANNOTATE REPEAT EXPANSIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

if (!params.skip_repeat_analysis && params.analysis_type.equals("wgs") ) {
CALL_REPEAT_EXPANSIONS (
ch_mapped.genome_bam_bai,
ch_variant_catalog,
Expand All @@ -420,49 +433,132 @@ workflow RAREDISEASE {
ch_versions = ch_versions.mix(CALL_REPEAT_EXPANSIONS.out.versions)
}

//
// SNV CALLING
//
CALL_SNV (
ch_mapped.genome_bam_bai,
ch_mapped.mt_bam_bai,
ch_mapped.mtshift_bam_bai,
ch_genome_chrsizes,
ch_genome_fasta,
ch_genome_fai,
ch_genome_dictionary,
ch_mt_intervals,
ch_mtshift_fasta,
ch_mtshift_fai,
ch_mtshift_dictionary,
ch_mtshift_intervals,
ch_mtshift_backchain,
ch_dbsnp,
ch_dbsnp_tbi,
ch_call_interval,
ch_ml_model,
ch_case_info,
ch_foundin_header,
Channel.value(params.sentieon_dnascope_pcr_indel_model)
)
ch_versions = ch_versions.mix(CALL_SNV.out.versions)

//
// VARIANT EVALUATION
//
if (params.run_rtgvcfeval) {
VARIANT_EVALUATION (
CALL_SNV.out.genome_vcf_tabix,
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CALL AND ANNOTATE NUCLEAR AND MITOCHONDRIAL SNVs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

if (!params.skip_snv_calling) {
CALL_SNV (
ch_mapped.genome_bam_bai,
ch_mapped.mt_bam_bai,
ch_mapped.mtshift_bam_bai,
ch_genome_chrsizes,
ch_genome_fasta,
ch_genome_fai,
ch_rtg_truthvcfs,
ch_sdf
ch_genome_dictionary,
ch_mt_intervals,
ch_mtshift_fasta,
ch_mtshift_fai,
ch_mtshift_dictionary,
ch_mtshift_intervals,
ch_mtshift_backchain,
ch_dbsnp,
ch_dbsnp_tbi,
ch_call_interval,
ch_ml_model,
ch_case_info,
ch_foundin_header,
Channel.value(params.sentieon_dnascope_pcr_indel_model)
)
ch_versions = ch_versions.mix(VARIANT_EVALUATION.out.versions)
ch_versions = ch_versions.mix(CALL_SNV.out.versions)

//
// ANNOTATE GENOME SNVs
//
if (!params.skip_snv_annotation) {

ANNOTATE_GENOME_SNVS (
CALL_SNV.out.genome_vcf_tabix,
params.analysis_type,
ch_cadd_header,
ch_cadd_resources,
ch_vcfanno_resources,
ch_vcfanno_lua,
ch_vcfanno_toml,
params.genome,
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_gnomad_af,
ch_samples,
ch_scatter_split_intervals,
ch_vep_extra_files,
ch_genome_chrsizes
).set { ch_snv_annotate }
ch_versions = ch_versions.mix(ch_snv_annotate.versions)

GENERATE_CLINICAL_SET_SNV(
ch_snv_annotate.vcf_ann,
ch_hgnc_ids
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions)

ANN_CSQ_PLI_SNV (
GENERATE_CLINICAL_SET_SNV.out.vcf,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)

RANK_VARIANTS_SNV (
ANN_CSQ_PLI_SNV.out.vcf_ann,
ch_pedfile,
ch_reduced_penetrance,
ch_score_config_snv
)
ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions)
}

//
// ANNOTATE MT SNVs
//
if (!params.skip_mt_annotation && (params.run_mt_for_wes || params.analysis_type.equals("wgs"))) {

ANNOTATE_MT_SNVS (
CALL_SNV.out.mt_vcf,
CALL_SNV.out.mt_tabix,
ch_cadd_header,
ch_cadd_resources,
ch_genome_fasta,
ch_vcfanno_resources,
ch_vcfanno_toml,
params.genome,
params.vep_cache_version,
ch_vep_cache,
ch_vep_extra_files
).set { ch_mt_annotate }
ch_versions = ch_versions.mix(ch_mt_annotate.versions)

GENERATE_CLINICAL_SET_MT(
ch_mt_annotate.vcf_ann,
ch_hgnc_ids
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions)

ANN_CSQ_PLI_MT(
GENERATE_CLINICAL_SET_MT.out.vcf,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions)

RANK_VARIANTS_MT (
ANN_CSQ_PLI_MT.out.vcf_ann,
ch_pedfile,
ch_reduced_penetrance,
ch_score_config_mt
)
ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions)
}
}

//
// SV CALLING
//
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CALL AND ANNOTATE NUCLEAR AND MITOCHONDRIAL SVs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

CALL_STRUCTURAL_VARIANTS (
ch_mapped.genome_marked_bam,
ch_mapped.genome_marked_bai,
Expand Down Expand Up @@ -522,94 +618,8 @@ workflow RAREDISEASE {

}

//
// ANNOTATE GENOME SNVs
//
if (!params.skip_snv_annotation) {

ANNOTATE_GENOME_SNVS (
CALL_SNV.out.genome_vcf_tabix,
params.analysis_type,
ch_cadd_header,
ch_cadd_resources,
ch_vcfanno_resources,
ch_vcfanno_lua,
ch_vcfanno_toml,
params.genome,
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_gnomad_af,
ch_samples,
ch_scatter_split_intervals,
ch_vep_extra_files,
ch_genome_chrsizes
).set { ch_snv_annotate }
ch_versions = ch_versions.mix(ch_snv_annotate.versions)

GENERATE_CLINICAL_SET_SNV(
ch_snv_annotate.vcf_ann,
ch_hgnc_ids
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions)

ANN_CSQ_PLI_SNV (
GENERATE_CLINICAL_SET_SNV.out.vcf,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions)

RANK_VARIANTS_SNV (
ANN_CSQ_PLI_SNV.out.vcf_ann,
ch_pedfile,
ch_reduced_penetrance,
ch_score_config_snv
)
ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions)

}

//
// ANNOTATE MT SNVs
//
if (!params.skip_mt_annotation && (params.run_mt_for_wes || params.analysis_type.equals("wgs"))) {

ANNOTATE_MT_SNVS (
CALL_SNV.out.mt_vcf,
CALL_SNV.out.mt_tabix,
ch_cadd_header,
ch_cadd_resources,
ch_genome_fasta,
ch_vcfanno_resources,
ch_vcfanno_toml,
params.genome,
params.vep_cache_version,
ch_vep_cache,
ch_vep_extra_files
).set { ch_mt_annotate }
ch_versions = ch_versions.mix(ch_mt_annotate.versions)

GENERATE_CLINICAL_SET_MT(
ch_mt_annotate.vcf_ann,
ch_hgnc_ids
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions)

ANN_CSQ_PLI_MT(
GENERATE_CLINICAL_SET_MT.out.vcf,
ch_variant_consequences_snv
)
ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions)

RANK_VARIANTS_MT (
ANN_CSQ_PLI_MT.out.vcf_ann,
ch_pedfile,
ch_reduced_penetrance,
ch_score_config_mt
)
ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions)

}

// STEP 1.7: SMNCOPYNUMBERCALLER
RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
Expand Down Expand Up @@ -710,6 +720,20 @@ workflow RAREDISEASE {

}
}

//
// VARIANT EVALUATION
//
if (params.run_rtgvcfeval) {
VARIANT_EVALUATION (
CALL_SNV.out.genome_vcf_tabix,
ch_genome_fai,
ch_rtg_truthvcfs,
ch_sdf
)
ch_versions = ch_versions.mix(VARIANT_EVALUATION.out.versions)
}

//
// Collate and save software versions
//
Expand Down
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