From 3af2b5288fa64913a85c42cda0423b63ffc03a03 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Sep 2024 13:58:54 +0200 Subject: [PATCH 01/14] add mito --- conf/modules/prepare_references.config | 10 ++--- nextflow_schema.json | 4 +- subworkflows/local/align.nf | 2 +- subworkflows/local/call_snv.nf | 4 +- .../local/call_structural_variants.nf | 45 +++++++++++-------- 5 files changed, 36 insertions(+), 29 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 401513ab..2793ec93 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -43,15 +43,15 @@ process { } withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' { - ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} } withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT_SHIFT' { - ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} } withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT' { - ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} } withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' { @@ -68,7 +68,7 @@ process { } withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT_SHIFT' { - ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes) } + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) } } withName: '.*PREPARE_REFERENCES:GATK_SD' { @@ -80,7 +80,7 @@ process { } withName: '.*PREPARE_REFERENCES:GATK_SD_MT_SHIFT' { - ext.when = { (params.analysis_type.equals("wgs") || params.run_mt_for_wes)} + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes)} } withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { diff --git a/nextflow_schema.json b/nextflow_schema.json index bf20ae91..d8be0ddb 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -485,9 +485,9 @@ "analysis_type": { "type": "string", "default": "wgs", - "description": "Specifies which analysis type for the pipeline- either 'wgs' or 'wes'. This changes resources consumed and tools used.", + "description": "Specifies which analysis type for the pipeline- either 'wgs', 'wes' or 'mito'. This changes resources consumed and tools used.", "fa_icon": "fas fa-align-center", - "enum": ["wgs", "wes"] + "enum": ["wgs", "wes", "mito"] }, "bwa_as_fallback": { "type": "boolean", diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf index 29c7f5da..d08b1cb5 100644 --- a/subworkflows/local/align.nf +++ b/subworkflows/local/align.nf @@ -83,7 +83,7 @@ workflow ALIGN { // PREPARING READS FOR MT ALIGNMENT - if (params.analysis_type.equals("wgs") || params.run_mt_for_wes) { + if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CONVERT_MT_BAM_TO_FASTQ ( ch_genome_bam_bai, ch_genome_fasta, diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 5d0b2ce9..23508848 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -46,7 +46,7 @@ workflow CALL_SNV { ch_sentieon_gvcf = Channel.empty() ch_sentieon_gtbi = Channel.empty() - if (params.variant_caller.equals("deepvariant")) { + if (params.variant_caller.equals("deepvariant") && !params.analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( // triggered only when params.variant_caller is set as deepvariant ch_genome_bam_bai, ch_genome_fasta, @@ -97,7 +97,7 @@ workflow CALL_SNV { ch_genome_tabix = GATK4_SELECTVARIANTS.out.tbi ch_genome_vcf_tabix = ch_genome_vcf.join(ch_genome_tabix, failOnMismatch:true, failOnDuplicate:true) - if (params.analysis_type.equals("wgs") || params.run_mt_for_wes) { + if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CALL_SNV_MT( ch_mt_bam_bai, ch_genome_fasta, diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 65f2f9ff..aca78e79 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -32,11 +32,16 @@ workflow CALL_STRUCTURAL_VARIANTS { main: ch_versions = Channel.empty() + ch_merged_svs = Channel.empty() + ch_merged_tbi = Channel.empty() - CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) - .diploid_sv_vcf - .collect{it[1]} - .set{ manta_vcf } + if (!params.analysis_type.equals("mito")) { + CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) + .diploid_sv_vcf + .collect{it[1]} + .set{ manta_vcf } + ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) + } if (params.analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info) @@ -61,7 +66,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions) } - if (params.analysis_type.equals("wgs") || params.run_mt_for_wes) { + if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } @@ -74,39 +79,41 @@ workflow CALL_STRUCTURAL_VARIANTS { .combine(cnvnator_vcf) .toList() .set { vcf_list } - } else { + } else if (!params.analysis_type.equals("mito")) { manta_vcf .toList() .set { vcf_list } } - } else if (params.analysis_type.equals("wgs")){ + } else if (params.analysis_type.equals("wgs")) { tiddit_vcf .combine(manta_vcf) .combine(gcnvcaller_vcf) .combine(cnvnator_vcf) .toList() .set { vcf_list } - } else { + } else if (!params.analysis_type.equals("mito")) { manta_vcf .combine(gcnvcaller_vcf) .toList() .set { vcf_list } } - ch_case_info - .combine(vcf_list) - .set { merge_input_vcfs } + if (!params.analysis_type.equals("mito")) { + ch_case_info + .combine(vcf_list) + .set { merge_input_vcfs } - SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority) + SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority) - TABIX_TABIX (SVDB_MERGE.out.vcf) - - ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) + TABIX_TABIX (SVDB_MERGE.out.vcf) + ch_merged_svs = SVDB_MERGE.out.vcf + ch_merged_tbi = TABIX_TABIX.out.tbi + ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) + ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) + } emit: - vcf = SVDB_MERGE.out.vcf // channel: [ val(meta), path(vcf)] - tbi = TABIX_TABIX.out.tbi // channel: [ val(meta), path(tbi)] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] versions = ch_versions // channel: [ path(versions.yml) ] } From a87672e117c90fa98fe1c7e199439d5e45533afa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Sep 2024 16:38:32 +0200 Subject: [PATCH 02/14] annotate --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 80e51572..ab4223ad 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -568,7 +568,7 @@ workflow RAREDISEASE { // // ANNOTATE MT SNVs // - if (!params.skip_mt_annotation && (params.run_mt_for_wes || params.analysis_type.equals("wgs"))) { + if (!params.skip_mt_annotation && (params.run_mt_for_wes || params.analysis_type.matches("wgs|mito"))) { ANNOTATE_MT_SNVS ( CALL_SNV.out.mt_vcf, From 6dacbb6acf52aaef500f5cbda9bcba21a60862d3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Sep 2024 16:49:54 +0200 Subject: [PATCH 03/14] bumpversion --- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dddb1aa8..a1451e1c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 2.3.0dev - Getafix [xxxx-xx-xx] + +### `Added` + +### `Changed` + +### `Fixed` + +### Parameters + +### Tool updates + ## 2.2.0 - Dogmatix [2024-09-13] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 964d29bf..b8bb11a1 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-raredisease-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index b6a62bee..33e4c551 100644 --- a/nextflow.config +++ b/nextflow.config @@ -307,7 +307,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.2.0' + version = '2.3.0dev' doi = '' } From 505c2b816842c6de891cce0824c918cfc4df2474 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 20 Sep 2024 10:25:01 +0200 Subject: [PATCH 04/14] align mt reads to mt and not genome --- conf/modules/prepare_references.config | 10 +++---- subworkflows/local/align.nf | 17 +++++++----- subworkflows/local/call_snv.nf | 19 +++++++------ subworkflows/local/prepare_references.nf | 34 +++++++++++++++++------- workflows/raredisease.nf | 19 ++++++++++--- 5 files changed, 68 insertions(+), 31 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 2793ec93..fd0e40f1 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -42,15 +42,15 @@ process { ext.when = {!params.bwa && (params.aligner == "sentieon" || params.mt_aligner == "sentieon")} } - withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' { + withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT.*' { ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} } - withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT_SHIFT' { + withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT.*' { ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} } - withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT' { + withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT.*' { ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} } @@ -67,7 +67,7 @@ process { ext.when = {!params.mt_fasta} } - withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT_SHIFT' { + withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT' { ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) } } @@ -79,7 +79,7 @@ process { ext.args = { "--interval-file-name ${meta.id}_mt" } } - withName: '.*PREPARE_REFERENCES:GATK_SD_MT_SHIFT' { + withName: '.*PREPARE_REFERENCES:GATK_SD_MT' { ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes)} } diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf index d08b1cb5..82f77f31 100644 --- a/subworkflows/local/align.nf +++ b/subworkflows/local/align.nf @@ -19,11 +19,16 @@ workflow ALIGN { ch_genome_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] ch_genome_bwamemeindex // channel: [mandatory] [ val(meta), path(index) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mt_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_mtshift_bwaindex // channel: [mandatory] [ val(meta), path(index) ] ch_mtshift_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] val_mbuffer_mem // integer: [mandatory] memory in megabytes val_platform // string: [mandatory] illumina or a different technology val_sort_threads // integer: [mandatory] memory in megabytes @@ -94,11 +99,11 @@ workflow ALIGN { ALIGN_MT ( CONVERT_MT_BAM_TO_FASTQ.out.fastq, CONVERT_MT_BAM_TO_FASTQ.out.bam, - ch_genome_bwaindex, - ch_genome_bwamem2index, - ch_genome_fasta, - ch_genome_dictionary, - ch_genome_fai + ch_mt_bwaindex, + ch_mt_bwamem2index, + ch_mt_fasta, + ch_mt_dictionary, + ch_mt_fai ) ALIGN_MT_SHIFT ( diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 23508848..8060e0cc 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -19,9 +19,12 @@ workflow CALL_SNV { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_mt_intervals // channel: [optional] [ path(interval_list) ] - ch_mtshift_fasta // channel: [optional] [ val(meta), path(fasta) ] - ch_mtshift_fai // channel: [optional] [ val(meta), path(fai) ] + ch_mt_dictionary // channel: [optional] [ val(meta), path(dict) ] + ch_mt_fai // channel: [optional] [ val(meta), path(fai) ] + ch_mt_fasta // channel: [optional] [ val(meta), path(fasta) ] ch_mtshift_dictionary // channel: [optional] [ val(meta), path(dict) ] + ch_mtshift_fai // channel: [optional] [ val(meta), path(fai) ] + ch_mtshift_fasta // channel: [optional] [ val(meta), path(fasta) ] ch_mtshift_intervals // channel: [optional] [ path(interval_list) ] ch_mtshift_backchain // channel: [mandatory] [ val(meta), path(back_chain) ] ch_dbsnp // channel: [optional] [ val(meta), path(vcf) ] @@ -100,9 +103,9 @@ workflow CALL_SNV { if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CALL_SNV_MT( ch_mt_bam_bai, - ch_genome_fasta, - ch_genome_fai, - ch_genome_dictionary, + ch_mt_fasta, + ch_mt_fai, + ch_mt_dictionary, ch_mt_intervals ) @@ -117,9 +120,9 @@ workflow CALL_SNV { POSTPROCESS_MT_CALLS( CALL_SNV_MT.out.vcf, CALL_SNV_MT_SHIFT.out.vcf, - ch_genome_fasta, - ch_genome_dictionary, - ch_genome_fai, + ch_mt_fasta, + ch_mt_dictionary, + ch_mt_fai, ch_mtshift_backchain, ch_case_info, ch_foundin_header, diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 8c39c614..4af09860 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -3,22 +3,25 @@ // include { BWA_INDEX as BWA_INDEX_GENOME } from '../../modules/nf-core/bwa/index/main' +include { BWA_INDEX as BWA_INDEX_MT } from '../../modules/nf-core/bwa/index/main' include { BWA_INDEX as BWA_INDEX_MT_SHIFT } from '../../modules/nf-core/bwa/index/main' include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../modules/nf-core/bwamem2/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../modules/nf-core/bwamem2/index/main' include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../modules/nf-core/bwamem2/index/main' include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME } from '../../modules/nf-core/bwameme/index/main' include { CAT_CAT as CAT_CAT_BAIT } from '../../modules/nf-core/cat/cat/main' include { GATK4_BEDTOINTERVALLIST as GATK_BILT } from '../../modules/nf-core/gatk4/bedtointervallist/main' include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD } from '../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT_SHIFT } from '../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../modules/nf-core/gatk4/createsequencedictionary/main' include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../modules/nf-core/gatk4/intervallisttools/main' include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../modules/nf-core/gatk4/shiftfasta/main' include { GET_CHROM_SIZES } from '../../modules/local/get_chrom_sizes' include { RTGTOOLS_FORMAT } from '../../modules/nf-core/rtgtools/format/main' include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../modules/nf-core/samtools/faidx/main' include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../modules/nf-core/samtools/faidx/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT_SHIFT } from '../../modules/nf-core/samtools/faidx/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../modules/nf-core/samtools/faidx/main' include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../modules/nf-core/sentieon/bwaindex/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../modules/nf-core/sentieon/bwaindex/main' include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../modules/nf-core/sentieon/bwaindex/main' include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/bgziptabix/main' @@ -66,11 +69,16 @@ workflow PREPARE_REFERENCES { // MT genome indices SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) ch_mt_fasta_in = Channel.empty().mix(ch_mt_fasta, SAMTOOLS_EXTRACT_MT.out.fa).collect() - SAMTOOLS_FAIDX_MT_SHIFT(ch_mt_fasta_in, [[],[]]) - GATK_SD_MT_SHIFT(ch_mt_fasta_in) - GATK_SHIFTFASTA(ch_mt_fasta_in, SAMTOOLS_FAIDX_MT_SHIFT.out.fai, GATK_SD_MT_SHIFT.out.dict) + SAMTOOLS_FAIDX_MT(ch_mt_fasta_in, [[],[]]) + GATK_SD_MT(ch_mt_fasta_in) + GATK_SHIFTFASTA(ch_mt_fasta_in, SAMTOOLS_FAIDX_MT.out.fai, GATK_SD_MT.out.dict) // MT alignment indices + BWAMEM2_INDEX_MT(ch_mt_fasta_in) + BWA_INDEX_MT(ch_mt_fasta_in) + SENTIEON_BWAINDEX_MT(ch_mt_fasta_in) + ch_bwa_mt = Channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() + BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) @@ -140,9 +148,12 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(GATK_SD.out.versions) ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT_SHIFT.out.versions) - ch_versions = ch_versions.mix(GATK_SD_MT_SHIFT.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions) + ch_versions = ch_versions.mix(GATK_SD_MT.out.versions) ch_versions = ch_versions.mix(GATK_SHIFTFASTA.out.versions) + ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions) + ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions) + ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions) ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT_SHIFT.out.versions) ch_versions = ch_versions.mix(BWA_INDEX_MT_SHIFT.out.versions) ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT_SHIFT.out.versions) @@ -167,11 +178,16 @@ workflow PREPARE_REFERENCES { genome_dict = ch_dict // channel: [ val(meta), path(dict) ] sdf = RTGTOOLS_FORMAT.out.sdf // channel: [ val (meta), path(intervals) ] mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] + mt_bwa_index = ch_bwa_mt // channel: [ val(meta), path(index) ] + mt_bwamem2_index = BWAMEM2_INDEX_MT.out.index.collect() // channel: [ val(meta), path(index) ] + mt_dict = GATK_SD_MT.out.dict.collect() // channel: [ val(meta), path(dict) ] + mt_fasta = ch_mt_fasta_in.collect() // channel: [ val(meta), path(fasta) ] + mt_fai = SAMTOOLS_FAIDX_MT.out.fai.collect() // channel: [ val(meta), path(fai) ] mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel: [ path(intervals) ] mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() // channel: [ val(meta), path(backchain) ] + mtshift_dict = GATK_SHIFTFASTA.out.dict // channel: [ val(meta), path(dict) ] mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() // channel: [ val(meta), path(fai) ] - mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel: [ val(meta), path(fai) ] - mtshift_dict = GATK_SHIFTFASTA.out.dict.collect() // channel: [ path(dict) ] + mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel: [ val(meta), path(fasta) ] mtshift_bwa_index = ch_bwa_mtshift // channel: [ val(meta), path(index) ] mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect() // channel: [ val(meta), path(index) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ab4223ad..c4fda9d1 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -271,6 +271,11 @@ workflow RAREDISEASE { ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it[0].simpleName], it]}.collect() : Channel.value([[:],[]]) ch_mt_intervals = ch_references.mt_intervals + ch_mt_bwaindex = ch_references.mt_bwa_index + ch_mt_bwamem2index = ch_references.mt_bwamem2_index + ch_mt_dictionary = ch_references.mt_dict + ch_mt_fai = ch_references.mt_fai + ch_mt_fasta = ch_references.mt_fasta ch_mtshift_backchain = ch_references.mtshift_backchain ch_mtshift_bwaindex = ch_references.mtshift_bwa_index ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index @@ -412,11 +417,16 @@ workflow RAREDISEASE { ch_genome_bwamem2index, ch_genome_bwamemeindex, ch_genome_dictionary, + ch_mt_bwaindex, + ch_mt_bwamem2index, + ch_mt_dictionary, + ch_mt_fai, + ch_mt_fasta, ch_mtshift_bwaindex, ch_mtshift_bwamem2index, - ch_mtshift_fasta, ch_mtshift_dictionary, ch_mtshift_fai, + ch_mtshift_fasta, params.mbuffer_mem, params.platform, params.samtools_sort_threads @@ -493,9 +503,12 @@ workflow RAREDISEASE { ch_genome_fai, ch_genome_dictionary, ch_mt_intervals, - ch_mtshift_fasta, - ch_mtshift_fai, + ch_mt_dictionary, + ch_mt_fai, + ch_mt_fasta, ch_mtshift_dictionary, + ch_mtshift_fai, + ch_mtshift_fasta, ch_mtshift_intervals, ch_mtshift_backchain, ch_dbsnp, From 9575a7f6f8efc21e870beecbb6774f0f290eb37e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 20 Sep 2024 10:31:55 +0200 Subject: [PATCH 05/14] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1451e1c..b9fb7e17 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- A new analysis option `mito` to call and annotate only mitochondrial variants [#608](https://github.com/nf-core/raredisease/pull/608) + ### `Changed` ### `Fixed` From 2bb4586481b10378be60801094edeee12727cdb2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 10:52:31 +0200 Subject: [PATCH 06/14] include filter --- conf/modules/generate_clinical_set.config | 8 +++++++- subworkflows/local/generate_clinical_set.nf | 15 ++++++++++++--- workflows/raredisease.nf | 9 ++++++--- 3 files changed, 25 insertions(+), 7 deletions(-) diff --git a/conf/modules/generate_clinical_set.config b/conf/modules/generate_clinical_set.config index de4d1b27..cb183ad1 100644 --- a/conf/modules/generate_clinical_set.config +++ b/conf/modules/generate_clinical_set.config @@ -50,10 +50,16 @@ process { process { withName: '.*:GENERATE_CLINICAL_SET_MT:ENSEMBLVEP_FILTERVEP' { ext.when = !params.skip_vep_filter - ext.prefix = { "${meta.id}_mt_${meta.set}" } + ext.prefix = { "${meta.id}_mt_filtervep_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } + withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_FILTER' { + ext.when = !params.skip_vep_filter + ext.prefix = { "${meta.id}_mt_${meta.set}" } + ext.args = { "-Oz -i 'AF>0.05'" } + } + withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIP' { ext.when = !params.skip_vep_filter ext.prefix = { "${meta.id}_mt_${meta.set}" } diff --git a/subworkflows/local/generate_clinical_set.nf b/subworkflows/local/generate_clinical_set.nf index 3e71e6b0..e4b94d8c 100644 --- a/subworkflows/local/generate_clinical_set.nf +++ b/subworkflows/local/generate_clinical_set.nf @@ -5,11 +5,13 @@ include { ENSEMBLVEP_FILTERVEP } from '../../modules/nf-core/ensemblvep/filtervep' include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip' include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix' +include { BCFTOOLS_FILTER } from '../../modules/nf-core/bcftools/filter' workflow GENERATE_CLINICAL_SET { take: ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_hgnc_ids // channel: [mandatory] [ val(hgnc_ids) ] + val_ismt // value: if mitochondria, set to true main: ch_versions = Channel.empty() @@ -28,16 +30,23 @@ workflow GENERATE_CLINICAL_SET { .output .set { ch_filtervep_out } - TABIX_BGZIP( ch_filtervep_out ) + if (val_ismt) { + BCFTOOLS_FILTER (ch_filtervep_out) + ch_clinical = BCFTOOLS_FILTER.out.vcf + ch_versions = ch_versions.mix( BCFTOOLS_FILTER.out.versions ) + } else { + TABIX_BGZIP( ch_filtervep_out ) + ch_clinical = TABIX_BGZIP.out.output + ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions ) + } ch_clin_research_vcf.research - .mix( TABIX_BGZIP.out.output ) + .mix( ch_clinical ) .set { ch_clin_research_split } TABIX_TABIX( ch_clin_research_split ) ch_versions = ch_versions.mix( ENSEMBLVEP_FILTERVEP.out.versions ) - ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions ) ch_versions = ch_versions.mix( TABIX_TABIX.out.versions ) emit: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index c4fda9d1..309f87d2 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -550,7 +550,8 @@ workflow RAREDISEASE { GENERATE_CLINICAL_SET_SNV( ch_snv_annotate.vcf_ann, - ch_hgnc_ids + ch_hgnc_ids, + false ) ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions) @@ -602,7 +603,8 @@ workflow RAREDISEASE { GENERATE_CLINICAL_SET_MT( ch_mt_annotate.vcf_ann, - ch_hgnc_ids + ch_hgnc_ids, + true ) ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions) @@ -677,7 +679,8 @@ workflow RAREDISEASE { GENERATE_CLINICAL_SET_SV( ch_sv_annotate.vcf_ann, - ch_hgnc_ids + ch_hgnc_ids, + false ) ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SV.out.versions) From 537de87ca4859e5a2e33d6954c379367193bc16d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:05:23 +0200 Subject: [PATCH 07/14] update usage docs --- docs/usage.md | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 0304c46a..70dbe8d4 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,24 +10,24 @@ Table of contents: - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data) - [Updating the pipeline](#updating-the-pipeline) - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data) - - [Samplesheet](#samplesheet) - - [Reference files and parameters](#reference-files-and-parameters) - - [1. Alignment](#1-alignment) - - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) - - [3. Repeat expansions](#3-repeat-expansions) - - [4. Variant calling - SNV](#4-variant-calling---snv) - - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) - - [6. Copy number variant calling](#6-copy-number-variant-calling) - - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) - - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) - - [9. Mitochondrial annotation](#9-mitochondrial-annotation) - - [10. Mobile element calling](#10-mobile-element-calling) - - [11. Mobile element annotation](#11-mobile-element-annotation) - - [12. Variant evaluation](#12-variant-evaluation) - - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) - - [Run the pipeline](#run-the-pipeline) - - [Direct input in CLI](#direct-input-in-cli) - - [Import from a config file (recommended)](#import-from-a-config-file-recommended) + - [Samplesheet](#samplesheet) + - [Reference files and parameters](#reference-files-and-parameters) + - [1. Alignment](#1-alignment) + - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) + - [3. Repeat expansions](#3-repeat-expansions) + - [4. Variant calling - SNV](#4-variant-calling---snv) + - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) + - [6. Copy number variant calling](#6-copy-number-variant-calling) + - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) + - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) + - [9. Mitochondrial annotation](#9-mitochondrial-annotation) + - [10. Mobile element calling](#10-mobile-element-calling) + - [11. Mobile element annotation](#11-mobile-element-annotation) + - [12. Variant evaluation](#12-variant-evaluation) + - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) + - [Run the pipeline](#run-the-pipeline) + - [Direct input in CLI](#direct-input-in-cli) + - [Import from a config file (recommended)](#import-from-a-config-file-recommended) - [Best practices](#best-practices) - [Core Nextflow arguments](#core-nextflow-arguments) - [`-profile`](#-profile) @@ -205,7 +205,7 @@ The mandatory and optional parameters for each category are tabulated below. 1Default variant caller is DeepVariant, but you have the option to use Sentieon as well.
2These parameters are only used by Sentieon.
-3Default is WGS, but you have the option to choose WES as well.
+3Default is `WGS`, but you have the option to choose `WES` and `mito` as well.
4This parameter is only used by Deepvariant.
##### 5. Variant calling - Structural variants From 099a566443660e9b0fd33927ff640c77336d6af5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:20:07 +0200 Subject: [PATCH 08/14] prettier --- docs/usage.md | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 70dbe8d4..c67e488b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,24 +10,24 @@ Table of contents: - [Run nf-core/raredisease with test data](#run-nf-coreraredisease-with-test-data) - [Updating the pipeline](#updating-the-pipeline) - [Run nf-core/raredisease with your data](#run-nf-coreraredisease-with-your-data) - - [Samplesheet](#samplesheet) - - [Reference files and parameters](#reference-files-and-parameters) - - [1. Alignment](#1-alignment) - - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) - - [3. Repeat expansions](#3-repeat-expansions) - - [4. Variant calling - SNV](#4-variant-calling---snv) - - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) - - [6. Copy number variant calling](#6-copy-number-variant-calling) - - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) - - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) - - [9. Mitochondrial annotation](#9-mitochondrial-annotation) - - [10. Mobile element calling](#10-mobile-element-calling) - - [11. Mobile element annotation](#11-mobile-element-annotation) - - [12. Variant evaluation](#12-variant-evaluation) - - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) - - [Run the pipeline](#run-the-pipeline) - - [Direct input in CLI](#direct-input-in-cli) - - [Import from a config file (recommended)](#import-from-a-config-file-recommended) + - [Samplesheet](#samplesheet) + - [Reference files and parameters](#reference-files-and-parameters) + - [1. Alignment](#1-alignment) + - [2. QC stats from the alignment files](#2-qc-stats-from-the-alignment-files) + - [3. Repeat expansions](#3-repeat-expansions) + - [4. Variant calling - SNV](#4-variant-calling---snv) + - [5. Variant calling - Structural variants](#5-variant-calling---structural-variants) + - [6. Copy number variant calling](#6-copy-number-variant-calling) + - [7. SNV annotation \& Ranking](#7-snv-annotation--ranking) + - [8. SV annotation \& Ranking](#8-sv-annotation--ranking) + - [9. Mitochondrial annotation](#9-mitochondrial-annotation) + - [10. Mobile element calling](#10-mobile-element-calling) + - [11. Mobile element annotation](#11-mobile-element-annotation) + - [12. Variant evaluation](#12-variant-evaluation) + - [13. Prepare data for CNV visualisation in Gens](#13-prepare-data-for-cnv-visualisation-in-gens) + - [Run the pipeline](#run-the-pipeline) + - [Direct input in CLI](#direct-input-in-cli) + - [Import from a config file (recommended)](#import-from-a-config-file-recommended) - [Best practices](#best-practices) - [Core Nextflow arguments](#core-nextflow-arguments) - [`-profile`](#-profile) From a57f931e76815c74b9e7ab9536dda2a39f113b18 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 14:42:07 +0200 Subject: [PATCH 09/14] update docs --- docs/output.md | 4 ++-- subworkflows/local/call_structural_variants.nf | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index d7f608b7..53f9a274 100644 --- a/docs/output.md +++ b/docs/output.md @@ -68,7 +68,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Hmtnote](#hmtnote) - [VEP](#vep-2) - [Filtering and ranking](#filtering-and-ranking) - - [Filter_vep](#filter_vep) + - [Filter\_vep](#filter_vep) - [GENMOD](#genmod) - [Mobile element analysis](#mobile-element-analysis) - [Calling mobile elements](#calling-mobile-elements) @@ -316,7 +316,7 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support. Output files - `call_sv/genome` - - `_sv_merge.vcf.gz`: file containing the merged variant calls. + - `_sv_merge.vcf.gz`: file containing the merged variant calls. As of version 2.3.0, this file also contains mitochondrial structural variants. - `_sv_merge.vcf.gz.tbi`: index of the file containing the merged variant calls. diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index aca78e79..c7d251b9 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -113,7 +113,7 @@ workflow CALL_STRUCTURAL_VARIANTS { } emit: - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - versions = ch_versions // channel: [ path(versions.yml) ] + versions = ch_versions // channel: [ path(versions.yml) ] } From 877cb317ed9f2380652deeaafef3d30393015b73 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 14:56:49 +0200 Subject: [PATCH 10/14] lint --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 53f9a274..1be5e4d5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -68,7 +68,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Hmtnote](#hmtnote) - [VEP](#vep-2) - [Filtering and ranking](#filtering-and-ranking) - - [Filter\_vep](#filter_vep) + - [Filter_vep](#filter_vep) - [GENMOD](#genmod) - [Mobile element analysis](#mobile-element-analysis) - [Calling mobile elements](#calling-mobile-elements) From c1ddf4c3e203a55bfb1b87d4d0239d70f77709c4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 15:23:02 +0200 Subject: [PATCH 11/14] changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b9fb7e17..b87230e4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Report only variants above 5% heteroplasmy in the clinical vcf file for mitochondria [#616](https://github.com/nf-core/raredisease/pull/616) + ### `Fixed` ### Parameters From 7d5e14e536c6412069cf790fe280cb7a4ee44fb5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 15:28:41 +0200 Subject: [PATCH 12/14] fix declaration error --- workflows/raredisease.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 309f87d2..88b75a3a 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -741,7 +741,8 @@ workflow RAREDISEASE { GENERATE_CLINICAL_SET_ME( ANNOTATE_MOBILE_ELEMENTS.out.vcf, - ch_hgnc_ids + ch_hgnc_ids, + false ) ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_ME.out.versions ) From 69eb6a1ea50da6cb8555116f7307dab9f642aa67 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 17:54:17 +0200 Subject: [PATCH 13/14] update docs --- docs/output.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index 1be5e4d5..1abe46b3 100644 --- a/docs/output.md +++ b/docs/output.md @@ -68,7 +68,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Hmtnote](#hmtnote) - [VEP](#vep-2) - [Filtering and ranking](#filtering-and-ranking) - - [Filter_vep](#filter_vep) + - [Filter\_vep](#filter_vep) - [GENMOD](#genmod) - [Mobile element analysis](#mobile-element-analysis) - [Calling mobile elements](#calling-mobile-elements) @@ -529,7 +529,7 @@ We recommend using vcfanno to annotate SNVs with precomputed CADD scores (files Output files - `rank_and_filter/` - - `_mt_ranked_clinical.vcf.gz`: file containing clinically relevant mitochondrial SNVs. + - `_mt_ranked_clinical.vcf.gz`: file containing clinically relevant mitochondrial SNVs, and only contains variants less than 5%VAF by default. - `_mt_ranked_clinical.vcf.gz.tbi`: index of the file containing clinically relevant mitochondrial SNVs. - `_mt_ranked_research.vcf.gz`: file containing mitochondrial SNV annotations with their rank scores. - `_mt_ranked_research.vcf.gz.tbi`: index of the file containing mitochondrial SNV annotations with their rank scores. From 931fc00ebe09db0961358467907784518a491393 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 24 Sep 2024 18:28:07 +0200 Subject: [PATCH 14/14] lint --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 1abe46b3..c96f5700 100644 --- a/docs/output.md +++ b/docs/output.md @@ -68,7 +68,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Hmtnote](#hmtnote) - [VEP](#vep-2) - [Filtering and ranking](#filtering-and-ranking) - - [Filter\_vep](#filter_vep) + - [Filter_vep](#filter_vep) - [GENMOD](#genmod) - [Mobile element analysis](#mobile-element-analysis) - [Calling mobile elements](#calling-mobile-elements)