From 42694e9dd4efd5254fb5d702009b963432203223 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Thu, 14 Nov 2024 10:24:40 +0100 Subject: [PATCH] review suggestions --- CHANGELOG.md | 44 ++++++++-------- conf/modules/qc_aligned_reads.config | 2 +- conf/test.config | 4 +- docs/parameters.md | 6 +-- docs/usage.md | 12 ++--- nextflow.config | 6 +-- nextflow_schema.json | 8 +-- .../local/utils_nfcore_nallo_pipeline/main.nf | 10 ++-- workflows/nallo.nf | 50 +++++++++---------- 9 files changed, 71 insertions(+), 71 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 018ff353..763650e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -62,7 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#411](https://github.com/genomic-medicine-sweden/nallo/pull/411) - Updated longphase module to most recent version. ([#409](https://github.com/genomic-medicine-sweden/nallo/issues/409)). - [#416](https://github.com/genomic-medicine-sweden/nallo/pull/416) - Updated WhatsHap to 2.3 and added the `--use-supplementary` flag to use supplementary reads for phasing by default. Changed modules to use biocontainers instead of custom containers. ([#296](https://github.com/genomic-medicine-sweden/nallo/issues/296)) - [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Updated SNV annotation tests to use correct configuration, and snapshot the md5sum, and summary of the variants -- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the default value of `--parallel_alignments` from 1 to 8, meaning the pipeline will perform parallel alignment by default +- [#418](https://github.com/genomic-medicine-sweden/nallo/pull/418) - Changed the default value of `--alignment_processes` from 1 to 8, meaning the pipeline will perform parallel alignment by default - [#422](https://github.com/genomic-medicine-sweden/nallo/pull/422) - Updated nf-core/tools template to v3.0.1 - [#423](https://github.com/genomic-medicine-sweden/nallo/pull/423) - Updated metro map - [#428](https://github.com/genomic-medicine-sweden/nallo/pull/428) - Changed from using bcftools to SVDB for SV merging @@ -125,25 +125,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `--validationSkipDuplicateCheck` | | | `--validationS3PathCheck` | | | `--monochromeLogs` | `--monochrome_logs` | -| `skip_short_variant_calling` | `skip_snv_calling` | -| `skip_assembly_wf` | `skip_genome_assembly` | -| `skip_mapping_wf` | `skip_alignment` | -| `skip_methylation_wf` | `skip_methylation_analysis` | -| `skip_phasing_wf` | `skip_phasing` | -| `variant_caller` | `snv_caller` | -| `parallel_snv` | `snv_calling_processes` | -| `cadd_prescored` | `cadd_prescored_indels` | -| `snp_db` | `echtvar_snv_databases` | -| `variant_catalog` | `stranger_repeat_catalog` | -| `bed` | `target_bed` | -| `hificnv_xy` | `hificnv_expected_xy_cn` | -| `hificnv_xx` | `hificnv_expected_xx_cn` | -| `hificnv_exclude` | `hificnv_excluded_regions` | -| `reduced_penetrance` | `genmod_reduced_penetrance` | -| `score_config_snv` | `genmod_score_config_snvs` | -| `score_config_sv` | `genmod_score_config_svs` | -| `parallel_alignments` | `alignment_processes` | -| `svdb_dbs` | `svdb_sv_databases` | +| `--skip_short_variant_calling` | `--skip_snv_calling` | +| `--skip_assembly_wf` | `--skip_genome_assembly` | +| `--skip_mapping_wf` | `--skip_alignment` | +| `--skip_methylation_wf` | `--skip_methylation_pileups` | +| `--skip_phasing_wf` | `--skip_phasing` | +| `--variant_caller` | `--snv_caller` | +| `--parallel_snv` | `--snv_calling_processes` | +| `--cadd_prescored` | `--cadd_prescored_indels` | +| `--snp_db` | `--echtvar_snv_databases` | +| `--variant_catalog` | `--stranger_repeat_catalog` | +| `--bed` | `--target_regions` | +| `--hificnv_xy` | `--hificnv_expected_xy_cn` | +| `--hificnv_xx` | `--hificnv_expected_xx_cn` | +| `--hificnv_exclude` | `--hificnv_excluded_regions` | +| `--reduced_penetrance` | `--genmod_reduced_penetrance` | +| `--score_config_snv` | `--genmod_score_config_snvs` | +| `--score_config_sv` | `--genmod_score_config_svs` | +| `--alignment_processes` | `--alignment_processes` | +| `--svdb_dbs` | `--svdb_sv_databases` | > [!NOTE] > Parameter has been updated if both old and new parameter information is present. @@ -247,7 +247,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#317](https://github.com/genomic-medicine-sweden/nallo/pull/317) - Changed so that `--reduced_penetrance` and `--score_config_snv` is required by rank variants and not SNV annotation - [#318](https://github.com/genomic-medicine-sweden/nallo/pull/318) - Updated docs and schema to clarify pipeline usage - [#321](https://github.com/genomic-medicine-sweden/nallo/pull/321) - Changed the input to BUILD_INTERVALS to have `meta.id` when building intervals from reference -- [#323](https://github.com/genomic-medicine-sweden/nallo/pull/323) - Changed `parallel_alignment` to `parallel_alignments` in CI tests as well +- [#323](https://github.com/genomic-medicine-sweden/nallo/pull/323) - Changed `parallel_alignment` to `alignment_processes` in CI tests as well - [#330](https://github.com/genomic-medicine-sweden/nallo/pull/330) - Updated README and version bump - [#332](https://github.com/genomic-medicine-sweden/nallo/pull/332) - Changed the PED file input to genmod to include inferred sex from somalier - [#333](https://github.com/genomic-medicine-sweden/nallo/pull/333) - Updated TRGT to 0.7.0 and added `meta.id` as output sample name @@ -282,7 +282,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | | `--skip_aligned_read_qc` | | | `--cadd_resources` | | | `--cadd_prescored` | -| `--split_fastq` | `--parallel_alignments` | +| `--split_fastq` | `--alignment_processes` | | `--extra_gvcfs` | | | `--extra_snfs` | | | `--dipcall_par` | `--par_regions` | diff --git a/conf/modules/qc_aligned_reads.config b/conf/modules/qc_aligned_reads.config index 5d116790..fd3746bb 100644 --- a/conf/modules/qc_aligned_reads.config +++ b/conf/modules/qc_aligned_reads.config @@ -41,7 +41,7 @@ process { ext.args = { [ '--fast-mode', '--no-per-base', - params.target_bed ? '' : '--by 500' + params.target_regions ? '' : '--by 500' ].join(' ') } publishDir = [ path: { "${params.outdir}/qc/mosdepth/${meta.id}" }, diff --git a/conf/test.config b/conf/test.config index 06eba183..86a53776 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,7 @@ params { // References fasta = params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz' input = params.pipelines_testdata_base_path + 'testdata/samplesheet.csv' - target_bed = params.pipelines_testdata_base_path + 'reference/test_data.bed' + target_regions = params.pipelines_testdata_base_path + 'reference/test_data.bed' hificnv_expected_xy_cn = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XY.bed' hificnv_expected_xx_cn = params.pipelines_testdata_base_path + 'reference/expected_cn.hg38.XX.bed' hificnv_excluded_regions = params.pipelines_testdata_base_path + 'reference/empty.bed' @@ -37,7 +37,7 @@ params { genmod_reduced_penetrance = params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv' genmod_score_config_snvs = params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini' genmod_score_config_svs = params.pipelines_testdata_base_path + 'reference/rank_model_svs.ini' - variant_consequences_snv = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' + variant_consequences_snvs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' variant_consequences_svs = params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt' somalier_sites = params.pipelines_testdata_base_path + 'reference/somalier_sites.vcf.gz' diff --git a/docs/parameters.md b/docs/parameters.md index f5aa2bc1..1956fe46 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -12,7 +12,7 @@ Allows skipping certain parts of the pipeline | `skip_snv_calling` | Skip short variant calling | `boolean` | False | | | | `skip_genome_assembly` | Skip genome assembly and assembly variant calling | `boolean` | False | | | | `skip_alignment` | Skip read mapping (alignment) | `boolean` | False | | | -| `skip_methylation_analysis` | Skip generation of methylation pileups | `boolean` | False | | | +| `skip_methylation_pileups` | Skip generation of methylation pileups | `boolean` | False | | | | `skip_repeat_calling` | Skip tandem repeat calling | `boolean` | False | | | | `skip_repeat_annotation` | Skip tandem repeat annotation | `boolean` | False | | | | `skip_phasing` | Skip phasing of variants and haplotagging of reads | `boolean` | False | | | @@ -40,10 +40,10 @@ Define where the pipeline should find input data and save output data. | `echtvar_snv_databases` | A csv file with echtvar databases to annotate SNVs with | `string` | | | | | `svdb_sv_databases` | Databases used for structural variant annotation in vcf format.
HelpPath to comma-separated file containing information about the databases used for structural variant annotation.
| `string` | | | | | `stranger_repeat_catalog` | A variant catalog json-file for stranger | `string` | | | | -| `variant_consequences_snv` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | +| `variant_consequences_snvs` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | | `variant_consequences_svs` | File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html | `string` | | | | | `vep_cache` | A path to the VEP cache location | `string` | | | | -| `bed` | A BED file with regions of interest, used to limit short variant calling. | `string` | | | | +| `target_regions` | A BED file with regions of interest, used to limit variant calling. | `string` | | | | | `hificnv_expected_xy_cn` | A BED file containing expected copy number regions for XY samples. | `string` | | | | | `hificnv_expected_xx_cn` | A BED file containing expected copy number regions for XX samples. | `string` | | | | | `hificnv_excluded_regions` | A BED file specifying regions to exclude with HiFiCNV, such as centromeres. | `string` | | | | diff --git a/docs/usage.md b/docs/usage.md index ffe5ae66..53def5eb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -89,7 +89,7 @@ This pipeline comes with three different presets that should be set with the `-- The selected preset will turn off subworkflows: - `--skip_genome_assembly` and `--skip_repeat_wf` will be set to `true` for `ONT_R10` - - `--skip_methylation_analysis` will be set to `true` for `pacbio` + - `--skip_methylation_pileups` will be set to `true` for `pacbio` ## Subworkflows @@ -117,7 +117,7 @@ For example, `nextflow run genomic-medicine-sweden/nallo -profile docker --outdi ``` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - --skip_alignment is active, the pipeline has to be run with: --skip_qc --skip_genome_assembly --skip_call_paralogs --skip_snv_calling --skip_snv_annotation --skip_cnv_calling --skip_phasing --skip_rank_variants --skip_repeat_calling --skip_repeat_annotation --skip_methylation_analysis + --skip_alignment is active, the pipeline has to be run with: --skip_qc --skip_genome_assembly --skip_call_paralogs --skip_snv_calling --skip_snv_annotation --skip_cnv_calling --skip_phasing --skip_rank_variants --skip_repeat_calling --skip_repeat_annotation --skip_methylation_pileups ... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` @@ -202,7 +202,7 @@ Turned off with `--skip_phasing`. This subworkflow relies on mapping and short variant calling subworkflows, but requires no additional files. -Turned off with `--skip_methylation_analysis`. +Turned off with `--skip_methylation_pileups`. ### Repeat calling @@ -228,14 +228,14 @@ Turned off with `--skip_repeat_annotation`. This subworkflow relies on the mapping and short variant calling, and requires the following additional files: - + | Parameter | Description | | ------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `vep_cache` | VEP cache matching your reference genome, either as a `.tar.gz` archive or path to a directory (e.g. [homo_sapiens_vep_110_GRCh38.tar.gz](https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz)) | | `vep_plugin_files` 1 | A csv file with VEP plugin files, pLI and LoFtool are required. Example provided below. | | `echtvar_snv_databases` 2 |  A csv file with annotation databases from ([`echtvar encode`](https://github.com/brentp/echtvar)) | -| `variant_consequences_snv` | A list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://ensembl.org/info/genome/variation/prediction/predicted_data.html) | +| `variant_consequences_snvs` | A list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://ensembl.org/info/genome/variation/prediction/predicted_data.html) | 1 Example file for input with `--vep_plugin_files` @@ -311,7 +311,7 @@ This subworkflow ranks SVs, and relies on the mapping, SV calling and SV annotat ## Other highlighted parameters -- Limit SNV calling to regions in BED file (`--bed`). +- Limit SNV calling to regions in BED file (`--target_bed`). - By default SNV-calling is split into 13 parallel processes, this speeds up the variant calling significantly. Limit this by setting `--snv_calling_processes` to a different number. - By default the pipeline splits the input files into eight pieces, performs parallel alignment and then merges the files. This can be changed to a different number with `--alignment_processes`, or turned off by supplying a value of 1. Parallel alignment comes with some additional overhead, but can speed up the pipeline significantly. diff --git a/nextflow.config b/nextflow.config index 430d7e02..f13d5315 100644 --- a/nextflow.config +++ b/nextflow.config @@ -11,7 +11,7 @@ params { // Input options input = null - target_bed = null + target_regions = null cadd_resources = null cadd_prescored_indels = null par_regions = null @@ -23,7 +23,7 @@ params { genmod_score_config_svs = null echtvar_snv_databases = null svdb_sv_databases = null - variant_consequences_snv = null + variant_consequences_snvs = null variant_consequences_svs = null vep_cache = null vep_plugin_files = null @@ -37,7 +37,7 @@ params { skip_call_paralogs = false skip_cnv_calling = false skip_alignment = false - skip_methylation_analysis = params.preset == 'pacbio' ? true : false + skip_methylation_pileups = params.preset == 'pacbio' ? true : false skip_phasing = false skip_qc = false skip_rank_variants = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 180ec1a8..5a039737 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -35,7 +35,7 @@ "fa_icon": "fas fa-fast-forward", "default": false }, - "skip_methylation_analysis": { + "skip_methylation_pileups": { "type": "boolean", "description": "Skip generation of methylation pileups", "fa_icon": "fas fa-fast-forward", @@ -184,7 +184,7 @@ "format": "file-path", "exists": true }, - "variant_consequences_snv": { + "variant_consequences_snvs": { "type": "string", "description": "File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SNVs. For more information check https://ensembl.org/info/genome/variation/prediction/predicted_data.html", "fa_icon": "fas fa-file-csv" @@ -200,7 +200,7 @@ "format": "path", "exists": true }, - "target_bed": { + "target_regions": { "type": "string", "pattern": "^\\S+\\.bed$", "format": "file-path", @@ -465,7 +465,7 @@ "vep_plugin_files": { "type": "string", "mimetype": "text/csv", - "description": "A csv file with vep_plugin_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required.", + "description": "A csv file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required.", "schema": "assets/vep_plugin_files_schema.json" }, "deepvariant_model_type": { diff --git a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 69933320..1561771c 100644 --- a/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -43,7 +43,7 @@ def workflowSkips = [ rank_variants : "skip_rank_variants", repeat_calling : "skip_repeat_calling", repeat_annotation: "skip_repeat_annotation", - methylation : "skip_methylation_analysis", + methylation : "skip_methylation_pileups", qc : "skip_qc", ] @@ -72,7 +72,7 @@ def fileDependencies = [ mapping : ["fasta", "somalier_sites"], assembly : ["fasta", "par_regions"], // The assembly workflow should be split into two - assembly and variant calling (requires ref) snv_calling : ["fasta", "par_regions"], - snv_annotation : ["echtvar_snv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_snv"], + snv_annotation : ["echtvar_snv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_snvs"], sv_annotation : ["svdb_sv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_svs"], cnv_calling : ["hificnv_expected_xy_cn", "hificnv_expected_xx_cn", "hificnv_excluded_regions"], rank_variants : ["genmod_reduced_penetrance", "genmod_score_config_snvs", "genmod_score_config_svs"], @@ -84,7 +84,7 @@ def parameterStatus = [ workflow: [ skip_snv_calling : params.skip_snv_calling, skip_phasing : params.skip_phasing, - skip_methylation_analysis: params.skip_methylation_analysis, + skip_methylation_pileups: params.skip_methylation_pileups, skip_rank_variants : params.skip_rank_variants, skip_repeat_calling : params.skip_repeat_calling, skip_repeat_annotation : params.skip_repeat_annotation, @@ -111,7 +111,7 @@ def parameterStatus = [ genmod_reduced_penetrance: params.genmod_reduced_penetrance, genmod_score_config_snvs : params.genmod_score_config_snvs, genmod_score_config_svs : params.genmod_score_config_svs, - variant_consequences_snv : params.variant_consequences_snv, + variant_consequences_snvs : params.variant_consequences_snvs, variant_consequences_svs : params.variant_consequences_svs, ] ] @@ -418,7 +418,7 @@ def toolCitationText() { "LongPhase (Lin et al. 2024)", ] } - if (!params.skip_methylation_analysis) { + if (!params.skip_methylation_pileups) { citation_text = citation_text + [ "modkit", "Tabix (Li 2011)", diff --git a/workflows/nallo.nf b/workflows/nallo.nf index c84047b9..99644c94 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -81,11 +81,11 @@ workflow NALLO { ch_cadd_prescored_indels = createReferenceChannelFromPath(params.cadd_prescored_indels) ch_fasta = createReferenceChannelFromPath(params.fasta) ch_tandem_repeats = createReferenceChannelFromPath(params.tandem_repeats, Channel.value([[],[]])) - ch_input_bed = createReferenceChannelFromPath(params.target_bed, Channel.value([[],[]])) + ch_input_bed = createReferenceChannelFromPath(params.target_regions, Channel.value([[],[]])) ch_par = createReferenceChannelFromPath(params.par_regions) ch_trgt_bed = createReferenceChannelFromPath(params.trgt_repeats) ch_stranger_repeat_catalog = createReferenceChannelFromPath(params.stranger_repeat_catalog) - ch_variant_consequences_snv = createReferenceChannelFromPath(params.variant_consequences_snv) + ch_variant_consequences_snvs = createReferenceChannelFromPath(params.variant_consequences_snvs) ch_variant_consequences_svs = createReferenceChannelFromPath(params.variant_consequences_svs) ch_vep_cache_unprocessed = createReferenceChannelFromPath(params.vep_cache, Channel.value([])) ch_expected_xy_bed = createReferenceChannelFromPath(params.hificnv_expected_xy_cn) @@ -110,7 +110,7 @@ workflow NALLO { CONVERT_INPUT_FILES ( ch_input, !params.skip_genome_assembly, // should bam -> fastq conversion be done - !params.skip_mapping_wf // should fastq -> bam conversion be done + !params.skip_alignment // should fastq -> bam conversion be done ) ch_versions = ch_versions.mix(CONVERT_INPUT_FILES.out.versions) @@ -134,7 +134,7 @@ workflow NALLO { mmi = PREPARE_GENOME.out.mmi // Split input files for alignment - if (params.parallel_alignment_processes > 1) { + if (params.alignment_processes > 1) { SPLITUBAM ( CONVERT_INPUT_FILES.out.bam ) ch_versions = ch_versions.mix(SPLITUBAM.out.versions) @@ -144,7 +144,7 @@ workflow NALLO { // Align reads (could be a split-align-merge subworkflow) // MINIMAP2_ALIGN ( - params.parallel_alignments > 1 ? SPLITUBAM.out.bam.transpose() : CONVERT_INPUT_FILES.out.bam, + params.alignment_processes > 1 ? SPLITUBAM.out.bam.transpose() : CONVERT_INPUT_FILES.out.bam, mmi, true, 'bai', @@ -251,7 +251,7 @@ workflow NALLO { // // Hifiasm assembly and assembly variant calling // - if(!params.skip_assembly_wf) { + if(!params.skip_genome_assembly) { //Hifiasm assembly ASSEMBLY( CONVERT_INPUT_FILES.out.fastq ) @@ -283,17 +283,17 @@ workflow NALLO { // if(!params.skip_snv_calling) { - // - // Make BED intervals, to be used for parallel SNV calling - // - SCATTER_GENOME ( - fai, - ch_input_bed, - !params.bed, - !params.skip_short_variant_calling, - params.parallel_snv - ) - ch_versions = ch_versions.mix(SCATTER_GENOME.out.versions) + // + // Make BED intervals, to be used for parallel SNV calling + // + SCATTER_GENOME ( + fai, + ch_input_bed, // BED file to scatter + !params.target_regions, // Make bed from fai + !params.skip_snv_calling, + params.snv_calling_processes + ) + ch_versions = ch_versions.mix(SCATTER_GENOME.out.versions) // Combine to create a bam_bai - interval pair for each sample bam_bai @@ -337,7 +337,7 @@ workflow NALLO { ANN_CSQ_PLI_SNV ( SNV_ANNOTATION.out.vcf, - ch_variant_consequences_snv + ch_variant_consequences_snvs ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) @@ -375,8 +375,8 @@ workflow NALLO { RANK_VARIANTS_SNV ( ANN_CSQ_PLI_SNV.out.vcf, rank_snvs_ped_in, - ch_reduced_penetrance, - ch_score_config_snv + ch_genmod_reduced_penetrance, + ch_genmod_score_config_snvs ) ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) @@ -388,7 +388,7 @@ workflow NALLO { // // Concatenate, sort, split, make database and get statistics of SNVs (should be a subworkflow) // - if(!params.skip_short_variant_calling) { + if(!params.skip_snv_calling) { ch_vcf_tbi_per_region .map { meta, vcf, tbi -> [ [ id: meta.project ], vcf, tbi ] } @@ -424,7 +424,7 @@ workflow NALLO { // // Call SVs // - if(!params.skip_mapping_wf) { + if(!params.skip_alignment) { // If both CNV-calling and SV annotation is off, merged variants are output from here CALL_SVS ( @@ -527,8 +527,8 @@ workflow NALLO { RANK_VARIANTS_SVS ( ANN_CSQ_PLI_SVS.out.vcf, SOMALIER_PED_FAMILY.out.ped, - ch_reduced_penetrance, - ch_score_config_svs + ch_genmod_reduced_penetrance, + ch_genmod_score_config_svs ) ch_versions = ch_versions.mix(RANK_VARIANTS_SVS.out.versions) } @@ -554,7 +554,7 @@ workflow NALLO { // // Create methylation pileups with modkit // - if(!params.skip_methylation_analysis) { + if(!params.skip_methylation_pileups) { METHYLATION ( !params.skip_phasing ? PHASING.out.haplotagged_bam_bai : bam_bai, fasta,