Skip to content

Commit

Permalink
Merge branch 'dev' into update_modules
Browse files Browse the repository at this point in the history
  • Loading branch information
@jemten
jemten authored Jan 26, 2024
2 parents 2b76d6b + d244293 commit 76390a0
Show file tree
Hide file tree
Showing 12 changed files with 258 additions and 215 deletions.
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Changed the name of the parameter from `skip_cnv_calling` to `skip_germlinecnvcaller` [#435](https://github.com/nf-core/raredisease/pull/435)
- Check SVDB query input files for existence and correct format [#476](https://github.com/nf-core/raredisease/pull/476)
- Change hardcoded platform value to params.platform in align_MT.config [#475](https://github.com/nf-core/raredisease/pull/475)
- The split into clincial and research VCFs is now done before ranking the varaints [#485](https://github.com/nf-core/raredisease/pull/485)
- Installed the nf-core version of ensemblvep/vep module [#482](https://github.com/nf-core/raredisease/pull/482)
- The filenames of the ranked output VCF files have been changed. See [output.md](docs/output.md#filtering-and-ranking) for more information[#485](https://github.com/nf-core/raredisease/pull/485)

### `Fixed`

Expand Down
33 changes: 9 additions & 24 deletions conf/modules/annotate_consequence_pli.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,20 +21,15 @@ process {
}

withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ' {
ext.prefix = { "${meta.id}_genome_vep_csq" }
ext.prefix = { "${meta.id}_sv_csq_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_PLI' {
ext.prefix = { "${meta.id}_genome_vep_csq_pli" }
ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_SV:TABIX_BGZIPTABIX' {
ext.prefix = { "${meta.id}_genome_vep_csq_pli" }
publishDir = [
path: { "${params.outdir}/annotate_sv" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" }
}
}
}
Expand All @@ -49,20 +44,15 @@ process {
}

withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_CSQ' {
ext.prefix = { "${meta.id}_vep_csq" }
ext.prefix = { "${meta.id}_snv_csq_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_PLI' {
ext.prefix = { "${meta.id}_vep_csq_pli" }
ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' {
ext.prefix = { "${meta.id}_vep_csq_pli" }
publishDir = [
path: { "${params.outdir}/annotate_snv/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" }
}
}
}
Expand All @@ -77,20 +67,15 @@ process {
}

withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_CSQ' {
ext.prefix = { "${meta.id}_mt_vep_csq" }
ext.prefix = { "${meta.id}_mt_csq_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_PLI' {
ext.prefix = { "${meta.id}_mt_vep_csq_pli" }
ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" }
}

withName: '.*ANN_CSQ_PLI_MT:TABIX_BGZIPTABIX' {
ext.prefix = { "${meta.id}_mt_vep_csq_pli" }
publishDir = [
path: { "${params.outdir}/annotate_snv/genome" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" }
}
}
}
7 changes: 6 additions & 1 deletion conf/modules/annotate_mobile_elements.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,12 +58,17 @@ process {
ext.prefix = { "${meta.id}_filter" }
}

withName: '.*ANNOTATE_MOBILE_ELEMENTS:FILTERVEP_ME' {
withName: '.*:ANNOTATE_MOBILE_ELEMENTS:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_me_${meta.set}" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*:ANNOTATE_MOBILE_ELEMENTS:GENERATE_CLINICAL_SET_ME:TABIX_BGZIP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_me_${meta.set}" }
}

withName: '.*ANNOTATE_MOBILE_ELEMENTS:ANNOTATE_CSQ_PLI_ME:ADD_MOST_SEVERE_CSQ' {
ext.prefix = { "${meta.id}_me_csq_${meta.set}" }
}
Expand Down
76 changes: 76 additions & 0 deletions conf/modules/generate_clinical_set.config
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.
ext.when = Conditional clause
----------------------------------------------------------------------------------------
*/

//
// Filter out clinical and research variants
//

// SNVs

process {
withName: '.*:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_snv_${meta.set}" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_snv_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}

// SVs

process {
withName: '.*:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_sv_${meta.set}" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*:GENERATE_CLINICAL_SET_SV:TABIX_BGZIP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_sv_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}

// MT variants

process {
withName: '.*:GENERATE_CLINICAL_SET_MT:ENSEMBLVEP_FILTERVEP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
48 changes: 32 additions & 16 deletions conf/modules/rank_variants.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,22 +24,30 @@ process {
}

withName: '.*RANK_VARIANTS_SV:GENMOD_ANNOTATE' {
ext.args = {
(params.genome == 'GRCh37') ? '--annotate_regions --genome-build 37' : '--annotate_regions --genome-build 38'
}
ext.prefix = { "${meta.id}_sv_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
].join(' ') }
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_snv_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
}

withName: '.*RANK_VARIANTS_SV:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_sv_genmod_score_${meta.set}" }
ext.args = " --rank_results "
}

withName: '.*RANK_VARIANTS_SV:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_ranked_sv" }
ext.prefix = { "${meta.id}_sv_genmod_compound_${meta.set}" }
}

withName: '.*RANK_VARIANTS_SV:BCFTOOLS_SORT' {
ext.args = "--output-type z"
ext.prefix = { "${meta.id}_ranked_sv" }
ext.prefix = { "${meta.id}_sv_ranked_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -75,29 +83,33 @@ process {
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_ANNOTATE' {
ext.args = {
(params.genome == 'GRCh37') ? '--annotate_regions --genome-build 37' : '--annotate_regions --genome-build 38'
}
ext.prefix = { "${meta.id}_snv_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
].join(' ') }
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_snv_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_snv_genmod_score_${meta.set}" }
ext.args = " --rank_results "
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_ranked_snv" }
ext.prefix = { "${meta.id}_snv_genmod_compound_${meta.set}" }
}

withName: '.*RANK_VARIANTS_SNV:BCFTOOLS_SORT' {
ext.when = false
}

withName: '.*RANK_VARIANTS_SNV:TABIX_BGZIP' {
ext.prefix = { "${meta.id}_ranked_snv" }
ext.prefix = { "${meta.id}_snv_ranked_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
Expand All @@ -122,36 +134,40 @@ process {
process {
if (!params.skip_mt_annotation) {
withName: '.*RANK_VARIANTS_MT:.*' {
ext.when = !params.skip_snv_annotation
ext.when = !params.skip_mt_annotation
publishDir = [
enabled: false
]
}

withName: '.*RANK_VARIANTS_MT:GENMOD_ANNOTATE' {
ext.args = {
(params.genome == 'GRCh37') ? '--annotate_regions --genome-build 37' : '--annotate_regions --genome-build 38'
}
ext.prefix = { "${meta.id}_mt_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
].join(' ') }
}

withName: '.*RANK_VARIANTS_MT:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_mt_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
}

withName: '.*RANK_VARIANTS_MT:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_mt_genmod_score_${meta.set}" }
ext.args = " --rank_results "
}

withName: '.*RANK_VARIANTS_MT:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_ranked_mt" }
ext.prefix = { "${meta.id}_mt_genmod_compound_${meta.set}" }
}

withName: '.*RANK_VARIANTS_MT:BCFTOOLS_SORT' {
ext.when = false
}

withName: '.*RANK_VARIANTS_MT:TABIX_BGZIP' {
ext.prefix = { "${meta.id}_ranked_mt" }
ext.prefix = { "${meta.id}_mt_ranked_${meta.set}" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
Expand Down
62 changes: 0 additions & 62 deletions conf/modules/raredisease.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,6 @@ process {
}
}



//
// Smncopynumbercaller options
//
Expand All @@ -63,66 +61,6 @@ process {
}
}

//
// Filter out clincal and research variants
//

process {

withName: '.*FILTERVEP_SNV' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_snv" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*BGZIPTABIX_SNV' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_snv" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}

process {

withName: '.*FILTERVEP_SV' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_sv" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*BGZIPTABIX_SV' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_sv" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}

process {
withName: '.*FILTERVEP_MT' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_mt" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*BGZIPTABIX_MT' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_clinical_mt" }
publishDir = [
path: { "${params.outdir}/rank_and_filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}

//
// Multiqc options
//
Expand Down
Loading

0 comments on commit 76390a0

Please sign in to comment.