From 2613281c7da6d814c98a9a1a1099d781d2fbd502 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Tue, 5 Jul 2022 06:49:49 +0000 Subject: [PATCH 01/13] add variant calling tool to vcf/bcftools + multiqc --- assets/multiqc_config.yml | 4 ++++ conf/modules.config | 4 ++-- .../nf-core/variantcalling/haplotypecaller/main.nf | 2 +- subworkflows/nf-core/variantcalling/tiddit/main.nf | 2 +- workflows/sarek.nf | 7 +++++++ 5 files changed, 15 insertions(+), 4 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6b6fdb1c7f..d2f497a7a8 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -56,6 +56,10 @@ module_order: extra_fn_clean_exts: - "_val" +fn_clean_sample_names: false + +use_filename_as_sample_name: true + sp: snpeff: contents: "SnpEff_version" diff --git a/conf/modules.config b/conf/modules.config index 56d8906196..328e1e3735 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1097,7 +1097,7 @@ process{ // VCF QC withName: 'BCFTOOLS_STATS'{ ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) } - ext.prefix = { "${vcf.baseName.minus(".vcf")}" } + ext.prefix = { "${meta.variantcaller}.${vcf.baseName.minus(".vcf")}" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/reports/bcftools" }, @@ -1107,7 +1107,7 @@ process{ withName: 'VCFTOOLS_.*'{ ext.when = { !(params.skip_tools && params.skip_tools.contains('vcftools')) } - ext.prefix = { "${variant_file.baseName.minus(".vcf")}" } + ext.prefix = { "${meta.variantcaller}.${variant_file.baseName.minus(".vcf")}" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/reports/vcftools" }, diff --git a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf index c82a6c7479..265784a370 100644 --- a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf +++ b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf @@ -108,7 +108,7 @@ workflow RUN_HAPLOTYPECALLER { known_sites, known_sites_tbi) - filtered_vcf = SINGLE_SAMPLE.out.filtered_vcf + filtered_vcf = SINGLE_SAMPLE.out.filtered_vcf.map{ meta, vcf-> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"haplotypecaller"], vcf]} ch_versions = ch_versions.mix(SINGLE_SAMPLE.out.versions) } diff --git a/subworkflows/nf-core/variantcalling/tiddit/main.nf b/subworkflows/nf-core/variantcalling/tiddit/main.nf index 77666df112..3ee6c76df8 100644 --- a/subworkflows/nf-core/variantcalling/tiddit/main.nf +++ b/subworkflows/nf-core/variantcalling/tiddit/main.nf @@ -18,7 +18,7 @@ workflow RUN_TIDDIT { TABIX_BGZIP_TIDDIT_SV(TIDDIT_SV.out.vcf) tiddit_ploidy = TIDDIT_SV.out.ploidy - tiddit_vcf_gz = TABIX_BGZIP_TIDDIT_SV.out.gz_tbi.map{ meta, gz, tbi -> [meta, gz]} + tiddit_vcf_gz = TABIX_BGZIP_TIDDIT_SV.out.gz_tbi.map{ meta, gz, tbi -> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"tiddit"], gz]} ch_versions = ch_versions.mix(TABIX_BGZIP_TIDDIT_SV.out.versions) ch_versions = ch_versions.mix(TIDDIT_SV.out.versions) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 67faad102e..ebdffd21d9 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -882,6 +882,8 @@ workflow SAREK { // ANNOTATE if (params.step == 'annotate') vcf_to_annotate = ch_input_sample + ch_input_sample.dump(tag:'ch_input_sample') + if (params.tools.contains('merge') || params.tools.contains('snpeff') || params.tools.contains('vep')) { ANNOTATE(vcf_to_annotate, @@ -899,8 +901,12 @@ workflow SAREK { ch_versions = ch_versions.mix(ANNOTATE.out.versions) ch_reports = ch_reports.mix(ANNOTATE.out.reports) + + } } + ch_reports.dump(tag:'ch_reports1') + ch_reports.collect().dump(tag:'ch_reports2') ch_version_yaml = Channel.empty() if (!(params.skip_tools && params.skip_tools.contains('versions'))) { @@ -919,6 +925,7 @@ workflow SAREK { ch_multiqc_config, ch_sarek_logo) + ch_multiqc_files.dump(tag:'multicq files') MULTIQC(ch_multiqc_files.collect()) multiqc_report = MULTIQC.out.report.toList() } From 1e6704c75f3cee259017e932834501beb7afc909 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 6 Jul 2022 14:30:45 +0000 Subject: [PATCH 02/13] fix vcftools + fix typos --- subworkflows/local/prepare_intervals.nf | 8 +++---- .../main.nf | 4 ++-- .../main.nf | 2 +- .../nf-core/variantcalling/tiddit/main.nf | 6 ++++- subworkflows/nf-core/vcf_qc.nf | 4 ++-- workflows/sarek.nf | 23 ++++++++++++------- 6 files changed, 29 insertions(+), 18 deletions(-) diff --git a/subworkflows/local/prepare_intervals.nf b/subworkflows/local/prepare_intervals.nf index b37511109d..2da68f065f 100644 --- a/subworkflows/local/prepare_intervals.nf +++ b/subworkflows/local/prepare_intervals.nf @@ -98,8 +98,8 @@ workflow PREPARE_INTERVALS { } emit: - intervals_bed = ch_intervals // path: intervals.bed, num_intervals [intervals split for parallel execution] - intervals_bed_gz_tbi = ch_intervals_bed_gz_tbi // path: target.bed.gz, target.bed.gz.tbi, num_intervals [intervals split for parallel execution] - intervals_bed_combined = ch_intervals_combined.map{meta, bed -> bed } // path: intervals.bed [all intervals in one file] - versions = ch_versions // channel: [ versions.yml ] + intervals_bed = ch_intervals // path: intervals.bed, num_intervals [intervals split for parallel execution] + intervals_bed_gz_tbi = ch_intervals_bed_gz_tbi // path: target.bed.gz, target.bed.gz.tbi, num_intervals [intervals split for parallel execution] + intervals_bed_combined = ch_intervals_combined.map{meta, bed -> bed }.collect() // path: intervals.bed [all intervals in one file] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf index 9669c616db..a3408f5fa1 100644 --- a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf @@ -80,7 +80,7 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING { MERGE_MUTECT2.out.tbi, mutect2_tbi_branch.no_intervals) - //Merge Muteect2 Stats + //Merge Mutect2 Stats MERGEMUTECTSTATS( mutect2_stats_branch.intervals .map{ meta, stats -> @@ -220,7 +220,7 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING { contamination_table = CALCULATECONTAMINATION.out.contamination // channel: [ val(meta), [ contamination ] ] segmentation_table = CALCULATECONTAMINATION.out.segmentation // channel: [ val(meta), [ segmentation ] ] - filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, gender:meta.gender, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:meta.num_intervals, variantcaller:"Mutect2"], + filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, gender:meta.gender, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:meta.num_intervals, variantcaller:"mutect2"], vcf]} // channel: [ val(meta), [ vcf ] ] filtered_tbi = FILTERMUTECTCALLS.out.tbi // channel: [ val(meta), [ tbi ] ] filtered_stats = FILTERMUTECTCALLS.out.stats // channel: [ val(meta), [ stats ] ] diff --git a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf index 34975771e9..1993195b9b 100644 --- a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf @@ -168,7 +168,7 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING { contamination_table = CALCULATECONTAMINATION.out.contamination // channel: [ val(meta), [ contamination ] ] segmentation_table = CALCULATECONTAMINATION.out.segmentation // channel: [ val(meta), [ segmentation ] ] - filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"Mutect2"] + filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"mutect2"] , vcf] } // channel: [ val(meta), [ vcf ] ] filtered_index = FILTERMUTECTCALLS.out.tbi // channel: [ val(meta), [ tbi ] ] filtered_stats = FILTERMUTECTCALLS.out.stats // channel: [ val(meta), [ stats ] ] diff --git a/subworkflows/nf-core/variantcalling/tiddit/main.nf b/subworkflows/nf-core/variantcalling/tiddit/main.nf index 3ee6c76df8..d4fc7eca2a 100644 --- a/subworkflows/nf-core/variantcalling/tiddit/main.nf +++ b/subworkflows/nf-core/variantcalling/tiddit/main.nf @@ -18,7 +18,11 @@ workflow RUN_TIDDIT { TABIX_BGZIP_TIDDIT_SV(TIDDIT_SV.out.vcf) tiddit_ploidy = TIDDIT_SV.out.ploidy - tiddit_vcf_gz = TABIX_BGZIP_TIDDIT_SV.out.gz_tbi.map{ meta, gz, tbi -> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"tiddit"], gz]} + tiddit_vcf_gz = TABIX_BGZIP_TIDDIT_SV.out.gz_tbi.map{ meta, gz, tbi -> + + new_meta = meta.tumor_id ? [patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:meta.num_intervals, variantcaller:'tiddit'] + : [patient:meta.patient, sample:meta.sample, status:meta.status, sex:meta.sex, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:'tiddit'] + [new_meta, gz]} ch_versions = ch_versions.mix(TABIX_BGZIP_TIDDIT_SV.out.versions) ch_versions = ch_versions.mix(TIDDIT_SV.out.versions) diff --git a/subworkflows/nf-core/vcf_qc.nf b/subworkflows/nf-core/vcf_qc.nf index 4765dc2087..ded381704e 100644 --- a/subworkflows/nf-core/vcf_qc.nf +++ b/subworkflows/nf-core/vcf_qc.nf @@ -14,8 +14,8 @@ workflow VCF_QC { BCFTOOLS_STATS(vcf) VCFTOOLS_TSTV_COUNT(vcf, target_bed, []) - VCFTOOLS_TSTV_QUAL(vcf, target_bed,[]) - VCFTOOLS_SUMMARY(vcf, target_bed,[]) + VCFTOOLS_TSTV_QUAL(vcf, target_bed, []) + VCFTOOLS_SUMMARY(vcf, target_bed, []) ch_versions = ch_versions.mix(BCFTOOLS_STATS.out.versions) ch_versions = ch_versions.mix(VCFTOOLS_TSTV_COUNT.out.versions) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index a6ec01b768..6e61300d2f 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -858,6 +858,8 @@ workflow SAREK { pon_tbi ) + //intervals_bed_combined.dump(tag:'intervals before pair variant calling') + //PREPARE_INTERVALS.out.intervals_bed_combined.dump(tag:'intervals before pair variant calling PREPARE INTERVALS:OUT') // PAIR VARIANT CALLING PAIR_VARIANT_CALLING( params.tools, @@ -908,7 +910,11 @@ workflow SAREK { ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions) //QC - VCF_QC(vcf_to_annotate, intervals_bed_combined) + //vcf_to_annotate.dump(tag:'vcf_to_annotate') + //intervals_bed_combined.dump(tag:'intervals bed combined') + //intervals_bed_combined.ifEmpty('intervals_bed_combined is empty"!!!!!!!!!!!!!!').view() + //PREPARE_INTERVALS.out.intervals_bed_combined.ifEmpty('intervals_bed_combined is empty PREPARE INTERVALS!!!!!!!!!!!!!!').view() + VCF_QC(vcf_to_annotate, PREPARE_INTERVALS.out.intervals_bed_combined) ch_versions = ch_versions.mix(VCF_QC.out.versions) ch_reports = ch_reports.mix(VCF_QC.out.bcftools_stats.collect{it[1]}.ifEmpty([])) @@ -916,12 +922,16 @@ workflow SAREK { ch_reports = ch_reports.mix(VCF_QC.out.vcftools_tstv_qual.collect{it[1]}.ifEmpty([])) ch_reports = ch_reports.mix(VCF_QC.out.vcftools_filter_summary.collect{it[1]}.ifEmpty([])) + //ch_reports.collect().dump(tag:'ch_reports after VCF_QC') + + VARIANTCALLING_CSV(vcf_to_annotate) + // ANNOTATE if (params.step == 'annotate') vcf_to_annotate = ch_input_sample - ch_input_sample.dump(tag:'ch_input_sample') + //ch_input_sample.dump(tag:'ch_input_sample') if (params.tools.contains('merge') || params.tools.contains('snpeff') || params.tools.contains('vep')) { @@ -939,13 +949,10 @@ workflow SAREK { // Gather used softwares versions ch_versions = ch_versions.mix(ANNOTATE.out.versions) ch_reports = ch_reports.mix(ANNOTATE.out.reports) - - - } } - ch_reports.dump(tag:'ch_reports1') - ch_reports.collect().dump(tag:'ch_reports2') + + //ch_reports.collect().dump(tag:'ch_reports2') ch_version_yaml = Channel.empty() if (!(params.skip_tools && params.skip_tools.contains('versions'))) { @@ -964,7 +971,7 @@ workflow SAREK { ch_multiqc_config, ch_sarek_logo) - ch_multiqc_files.dump(tag:'multicq files') + //ch_multiqc_files.dump(tag:'multicq files') MULTIQC(ch_multiqc_files.collect()) multiqc_report = MULTIQC.out.report.toList() } From 173f7b60668f82cc5d5d602c56a267bacc58e78a Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 6 Jul 2022 15:15:25 +0000 Subject: [PATCH 03/13] fix mutect + gender --- .../tumor_normal_somatic_variant_calling/main.nf | 2 +- .../tumor_only_somatic_variant_calling/main.nf | 2 +- .../nf-core/variantcalling/haplotypecaller/main.nf | 2 +- workflows/sarek.nf | 14 +++----------- 4 files changed, 6 insertions(+), 14 deletions(-) diff --git a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf index 57ad0e2981..e0ba046ea0 100644 --- a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf @@ -220,7 +220,7 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING { contamination_table = CALCULATECONTAMINATION.out.contamination // channel: [ val(meta), [ contamination ] ] segmentation_table = CALCULATECONTAMINATION.out.segmentation // channel: [ val(meta), [ segmentation ] ] - filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:meta.num_intervals, variantcaller:"Mutect2"], + filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:meta.num_intervals, variantcaller:"mutect2"], vcf]} // channel: [ val(meta), [ vcf ] ] filtered_tbi = FILTERMUTECTCALLS.out.tbi // channel: [ val(meta), [ tbi ] ] filtered_stats = FILTERMUTECTCALLS.out.stats // channel: [ val(meta), [ stats ] ] diff --git a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf index 534c9877db..d0aab00db5 100644 --- a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf +++ b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf @@ -168,7 +168,7 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING { contamination_table = CALCULATECONTAMINATION.out.contamination // channel: [ val(meta), [ contamination ] ] segmentation_table = CALCULATECONTAMINATION.out.segmentation // channel: [ val(meta), [ segmentation ] ] - filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, sample:meta.sample, status:meta.status, sex:meta.sex, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"Mutect2"] + filtered_vcf = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf -> [[patient:meta.patient, sample:meta.sample, status:meta.status, sex:meta.sex, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"mutect2"] , vcf] } // channel: [ val(meta), [ vcf ] ] filtered_index = FILTERMUTECTCALLS.out.tbi // channel: [ val(meta), [ tbi ] ] filtered_stats = FILTERMUTECTCALLS.out.stats // channel: [ val(meta), [ stats ] ] diff --git a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf index 5b3addb7cf..409523a76f 100644 --- a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf +++ b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf @@ -95,7 +95,7 @@ workflow RUN_HAPLOTYPECALLER { known_sites, known_sites_tbi) - filtered_vcf = SINGLE_SAMPLE.out.filtered_vcf.map{ meta, vcf-> [[patient:meta.patient, sample:meta.sample, status:meta.status, gender:meta.gender, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"haplotypecaller"], vcf]} + filtered_vcf = SINGLE_SAMPLE.out.filtered_vcf.map{ meta, vcf-> [[patient:meta.patient, sample:meta.sample, status:meta.status, sex:meta.sex, id:meta.sample, num_intervals:meta.num_intervals, variantcaller:"haplotypecaller"], vcf]} ch_versions = ch_versions.mix(SINGLE_SAMPLE.out.versions) } diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 062da856e3..bb130babba 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -921,11 +921,8 @@ workflow SAREK { ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions) //QC - //vcf_to_annotate.dump(tag:'vcf_to_annotate') - //intervals_bed_combined.dump(tag:'intervals bed combined') - //intervals_bed_combined.ifEmpty('intervals_bed_combined is empty"!!!!!!!!!!!!!!').view() - //PREPARE_INTERVALS.out.intervals_bed_combined.ifEmpty('intervals_bed_combined is empty PREPARE INTERVALS!!!!!!!!!!!!!!').view() - VCF_QC(vcf_to_annotate, PREPARE_INTERVALS.out.intervals_bed_combined) + vcf_to_annotate.dump(tag:'vcf_to_annotate') + VCF_QC(vcf_to_annotate, intervals_bed_combined) ch_versions = ch_versions.mix(VCF_QC.out.versions) ch_reports = ch_reports.mix(VCF_QC.out.bcftools_stats.collect{it[1]}.ifEmpty([])) @@ -933,17 +930,12 @@ workflow SAREK { ch_reports = ch_reports.mix(VCF_QC.out.vcftools_tstv_qual.collect{it[1]}.ifEmpty([])) ch_reports = ch_reports.mix(VCF_QC.out.vcftools_filter_summary.collect{it[1]}.ifEmpty([])) - //ch_reports.collect().dump(tag:'ch_reports after VCF_QC') - - VARIANTCALLING_CSV(vcf_to_annotate) // ANNOTATE if (params.step == 'annotate') vcf_to_annotate = ch_input_sample - //ch_input_sample.dump(tag:'ch_input_sample') - if (params.tools.contains('merge') || params.tools.contains('snpeff') || params.tools.contains('vep')) { ANNOTATE(vcf_to_annotate, @@ -963,7 +955,7 @@ workflow SAREK { } } - //ch_reports.collect().dump(tag:'ch_reports2') + ch_reports.collect().dump(tag:'ch_reports2') ch_version_yaml = Channel.empty() if (!(params.skip_tools && params.skip_tools.contains('versions'))) { From 71901f2a453662df71bf667215a24c0a02017b03 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Mon, 11 Jul 2022 16:02:34 +0000 Subject: [PATCH 04/13] update multiqc module --- assets/multiqc_config.yml | 47 +++++++++++++++++++----- conf/modules.config | 3 +- modules.json | 2 +- modules/nf-core/modules/multiqc/main.nf | 16 +++++--- modules/nf-core/modules/multiqc/meta.yml | 8 ++++ workflows/sarek.nf | 19 ++++++---- 6 files changed, 71 insertions(+), 24 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d2f497a7a8..28e60a1f6c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -6,11 +6,6 @@ report_comment: > This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation. -report_section_order: - software_versions: - order: -1000 - nf-core-sarek-summary: - order: -1001 export_plots: true @@ -39,9 +34,33 @@ module_order: name: "GATK4 MarkDuplicates" info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)." - samtools: - name: "Samtools Flagstat" + name: "Samtools Flagstat (mapped)" + fn: "*.md.cram.stats" + anchor: "md_stats" + info: "This section of the report shows mapped samtools stats." + path_filters: + - "*.md.cram.stats" + - mosdepth: + name: "Mosdepth (mapped)" + fn: "*.mapped.mosdepth.*.dist.txt" + anchor: "mapped_mosdepth" + info: "This section of the report shows the mapped distribution after mosdepth." + path_filters: + - "*.mapped.mosdepth.*.dist.txt" + - samtools: + name: "Samtools Flagstat (recal)" + fn: "*.recal.cram.stats" + anchor: "recal_stats" + info: "This section of the report shows recalibrated samtools stats." + path_filters: + - "*.recal.cram.stats" - mosdepth: - name: "Mosdepth" + name: "Mosdepth (recalibrated)" + fn: "*.recal.mosdepth.*.dist.txt" + anchor: "recal_mosdepth" + info: "This section of the report shows the recalibrated distribution after mosdepth." + path_filters: + - "*.recal.mosdepth.*.dist.txt" - gatk: name: "GATK4 BQSR" - bcftools: @@ -53,12 +72,22 @@ module_order: - vep: name: "VEP" +report_section_order: + md_stats: + before: recal_stats + mapped_mosdepth: + before: recal_mosdepth + software_versions: + order: -1000 + nf-core-sarek-summary: + order: -1001 + extra_fn_clean_exts: - "_val" -fn_clean_sample_names: false +#fn_clean_sample_names: false -use_filename_as_sample_name: true +#use_filename_as_sample_name: true sp: snpeff: diff --git a/conf/modules.config b/conf/modules.config index eebe7adfc9..7a85abdcc5 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1200,6 +1200,7 @@ process{ // MULTIQC withName:'MULTIQC' { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} - ext.args = { params.multiqc_config ? "--config $multiqc_custom_config" : "" } + //ext.args = { params.multiqc_config ? "--config $multiqc_custom_config" : "" } + //ext.args = '-d' } } diff --git a/modules.json b/modules.json index 9558720b38..a96625ff95 100644 --- a/modules.json +++ b/modules.json @@ -181,7 +181,7 @@ "git_sha": "f0800157544a82ae222931764483331a81812012" }, "multiqc": { - "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" + "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106" }, "samblaster": { "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf index ae019dbf0b..1e7d6afeae 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/modules/multiqc/main.nf @@ -1,13 +1,14 @@ process MULTIQC { label 'process_medium' - conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' : + 'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }" input: - path multiqc_files + path multiqc_files, stageAs: "?/*" + tuple path(multiqc_config), path(multiqc_logo) output: path "*multiqc_report.html", emit: report @@ -20,8 +21,13 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' """ - multiqc -f $args . + multiqc \\ + --force \\ + $config \\ + $args \\ + . cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml index 6fa891efc2..bf3a27fe73 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/modules/multiqc/meta.yml @@ -17,6 +17,14 @@ input: type: file description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Config yml for MultiQC + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Logo file for MultiQC + pattern: "*.{png}" output: - report: type: file diff --git a/workflows/sarek.nf b/workflows/sarek.nf index bb130babba..72c7b71685 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -273,9 +273,11 @@ include { MULTIQC } from '../module ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = Channel.fromPath(file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)) +ch_multiqc_config = [ + file("$projectDir/assets/multiqc_config.yml", checkIfExists: true), + file("$projectDir/assets/nf-core-sarek_logo_light.png", checkIfExists: true) + ] ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() -ch_sarek_logo = Channel.fromPath(file("$projectDir/assets/nf-core-sarek_logo_light.png", checkIfExists: true)) def multiqc_report = [] /* @@ -759,7 +761,7 @@ workflow SAREK { }.set{convert} //BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format - SAMTOOLS_BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai) + BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai) ch_versions = ch_versions.mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.versions) cram_variant_calling = Channel.empty().mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.alignment_index, convert.cram) @@ -968,14 +970,15 @@ workflow SAREK { ch_workflow_summary = Channel.value(workflow_summary) ch_multiqc_files = Channel.empty().mix(ch_version_yaml, + Channel.from(ch_multiqc_config), ch_multiqc_custom_config.collect().ifEmpty([]), ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'), - ch_reports.collect(), - ch_multiqc_config, - ch_sarek_logo) + ch_reports.collect() + ) - //ch_multiqc_files.dump(tag:'multicq files') - MULTIQC(ch_multiqc_files.collect()) + ch_multiqc_files.view() + + MULTIQC(ch_multiqc_files.collect(), ch_multiqc_config) multiqc_report = MULTIQC.out.report.toList() } } From 4e30625cb70aec796a69502775da5f4ae6e2af41 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 13 Jul 2022 10:49:29 +0000 Subject: [PATCH 05/13] update outputs varcallers + ci tests --- conf/modules.config | 76 +++++---- tests/test_tools.yml | 299 ++++++++++++++++++---------------- tests/test_tools_manually.yml | 24 +-- workflows/sarek.nf | 6 +- 4 files changed, 216 insertions(+), 189 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 7a85abdcc5..39986ca2f6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -514,6 +514,7 @@ process{ // DEEPVARIANT withName: 'MERGE_DEEPVARIANT_.*' { + ext.prefix = {"${meta.id}.deepvariant"} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" }, @@ -521,10 +522,10 @@ process{ ] } withName: 'MERGE_DEEPVARIANT_GVCF' { - ext.prefix = {"${meta.id}.g"} + ext.prefix = {"${meta.id}.deepvariant.g"} } withName: 'DEEPVARIANT' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}_${intervals.simpleName}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" } ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" } ext.when = { params.tools && params.tools.contains('deepvariant') } publishDir = [ @@ -535,6 +536,7 @@ process{ ] } withName : 'TABIX_VC_DEEPVARIANT_.*' { + ext.prefix = {"${meta.id}.deepvariant"} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" }, @@ -544,6 +546,7 @@ process{ // FREEBAYES withName: 'MERGE_FREEBAYES' { + ext.prefix = { "${meta.id}.freebayes" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }, @@ -551,8 +554,8 @@ process{ ] } withName: 'FREEBAYES' { - //To make sure no naming conflicts ensue with module BCFTOOLS_SORT & the naming being correct in the output folder - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${meta.id}_${target_bed.simpleName}.freebayes" } + //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" } ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1' ext.when = { params.tools && params.tools.contains('freebayes') } publishDir = [ @@ -561,7 +564,7 @@ process{ } withName: 'BCFTOOLS_SORT' { - ext.prefix = { "${vcf.baseName.minus(".freebayes.vcf")}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/" }, @@ -580,7 +583,7 @@ process{ // HAPLOTYPECALLER withName: 'MERGE_HAPLOTYPECALLER.*' { - ext.prefix = { params.joint_germline ? "${meta.id}.g" : "${meta.id}" } + ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" }, @@ -590,7 +593,7 @@ process{ withName: 'HAPLOTYPECALLER' { ext.args = { params.joint_germline ? "-ERC GVCF" : "" } - ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.g" : "${meta.id}" ) : ( params.joint_germline ? "${meta.id}_${intervals.simpleName}.g" :"${meta.id}_${intervals.simpleName}" ) } + ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) } ext.when = { params.tools && params.tools.contains('haplotypecaller') } publishDir = [ mode: params.publish_dir_mode, @@ -605,6 +608,7 @@ process{ ] } withName: 'FILTERVARIANTTRANCHES' { + ext.prefix = {"${meta.id}.haplotypecaller"} ext.args = { "--info-key CNN_1D" } publishDir = [ mode: params.publish_dir_mode, @@ -614,6 +618,7 @@ process{ } withName: 'GENOTYPEGVCFS' { + ext.prefix = {"${meta.id}.haplotypecaller"} ext.when = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline} publishDir = [ mode: params.publish_dir_mode, @@ -631,16 +636,16 @@ process{ ] } withName: 'MERGE_MANTA_DIPLOID' { - ext.prefix = {"${meta.id}.diploid_sv"} + ext.prefix = {"${meta.id}.manta.diploid_sv"} } withName: 'MERGE_MANTA_SMALL_INDELS' { - ext.prefix = {"${meta.id}.candidate_small_indels"} + ext.prefix = {"${meta.id}.manta.candidate_small_indels"} } withName: 'MERGE_MANTA_SV' { - ext.prefix = {"${meta.id}.candidate_sv"} + ext.prefix = {"${meta.id}.manta.candidate_sv"} } withName: 'MANTA.*' { - ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" } ext.args = { params.wes ? "--exome" : "" } ext.when = { params.tools && params.tools.contains('manta') } publishDir = [ @@ -660,13 +665,13 @@ process{ ] } withName: 'MERGE_STRELKA' { - ext.prefix = {"${meta.id}.variants"} + ext.prefix = {"${meta.id}.strelka.variants"} } withName: 'MERGE_STRELKA_GENOME' { - ext.prefix = {"${meta.id}.genome"} + ext.prefix = {"${meta.id}.strelka.genome"} } withName: 'STRELKA_.*' { - ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" } ext.args = { params.wes ? "--exome" : "" } ext.when = { params.tools && params.tools.contains('strelka') } publishDir = [ @@ -681,6 +686,7 @@ process{ withName: 'TIDDIT_SV' { ext.when = { params.tools && params.tools.contains('tiddit') } ext.args = { bwa_index ? "" : "--skip_assembly" } + ext.prefix = { "${meta.id}.tiddit" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }, @@ -688,7 +694,7 @@ process{ ] } withName : 'TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = { "${meta.id}.vcf" } + ext.prefix = { "${meta.id}.tiddit.vcf" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }, @@ -825,13 +831,14 @@ process{ //MANTA withName: 'MERGE_MANTA_TUMOR' { - ext.prefix = {"${meta.id}.tumor_sv"} + ext.prefix = {"${meta.id}.manta.tumor_sv"} } //MUTECT2 withName: 'CALCULATECONTAMINATION' { - ext.args = { "-tumor-segmentation ${meta.id}.segmentation.table" } - publishDir = [ + ext.prefix = { "${meta.id}.mutect2" } + ext.args = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" } + publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/" }, saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" } @@ -839,6 +846,7 @@ process{ } withName: 'MERGE_MUTECT2.*' { + ext.prefix = { "${meta.id}.mutect2" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }, @@ -847,7 +855,7 @@ process{ } withName: 'FILTERMUTECTCALLS.*'{ - ext.prefix = {"${meta.id}.filtered"} + ext.prefix = {"${meta.id}.mutect2.filtered"} publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/" }, @@ -856,6 +864,7 @@ process{ } withName: 'GATHERPILEUPSUMMARIES' { + ext.prefix = { "${meta.id}.mutect2" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }, @@ -864,6 +873,7 @@ process{ } withName: 'GATHERPILEUPSUMMARIES_.*' { + ext.prefix = { "${meta.id}.mutect2" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" }, @@ -872,7 +882,7 @@ process{ } withName: 'GETPILEUPSUMMARIES.*' { - ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/" }, @@ -882,6 +892,7 @@ process{ } withName: 'GETPILEUPSUMMARIES_.*' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/" }, @@ -891,7 +902,7 @@ process{ } withName: 'LEARNREADORIENTATIONMODEL'{ - ext.prefix = { "${meta.id}.artifactprior" } + ext.prefix = { "${meta.id}.mutect2.artifactprior" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }, @@ -900,7 +911,7 @@ process{ } withName: 'MERGEMUTECTSTATS' { - ext.prefix = { "${meta.id}" } + ext.prefix = { "${meta.id}.mutect2" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }, @@ -909,7 +920,7 @@ process{ } withName: 'MUTECT2'{ - ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" } + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } ext.when = { params.tools && params.tools.contains('mutect2') } ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" } publishDir = [ @@ -1042,7 +1053,7 @@ process{ //MANTA withName: 'MERGE_MANTA_SOMATIC' { - ext.prefix = {"${meta.id}.somatic_sv"} + ext.prefix = {"${meta.id}.manta.somatic_sv"} } //MUTECT2 @@ -1065,23 +1076,24 @@ process{ //STRELKA withName: 'MERGE_STRELKA_INDELS' { - ext.prefix = {"${meta.id}.somatic_indels"} + ext.prefix = {"${meta.id}.strelka.somatic_indels"} } withName: 'MERGE_STRELKA_SNVS' { - ext.prefix = {"${meta.id}.somatic_snvs"} + ext.prefix = {"${meta.id}.strelka.somatic_snvs"} } //TIDDIT withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.normal.vcf"} + ext.prefix = {"${meta.id}.tiddit.normal.vcf"} } withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.tumor.vcf"} + ext.prefix = {"${meta.id}.tiddit.tumor.vcf"} } //SVDB withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' { + ext.prefix = { "${meta.id}.tiddit" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }, @@ -1092,20 +1104,20 @@ process{ // VCF QC withName: 'BCFTOOLS_STATS'{ ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) } - ext.prefix = { "${meta.variantcaller}.${vcf.baseName.minus(".vcf")}" } + ext.prefix = { "${vcf.baseName.minus(".vcf")}" } publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/bcftools" }, + path: { "${params.outdir}/reports/bcftools/${meta.id}/${meta.variantcaller}/" }, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } withName: 'VCFTOOLS_.*'{ ext.when = { !(params.skip_tools && params.skip_tools.contains('vcftools')) } - ext.prefix = { "${meta.variantcaller}.${variant_file.baseName.minus(".vcf")}" } + ext.prefix = { "${variant_file.baseName.minus(".vcf")}" } publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/vcftools" }, + path: { "${params.outdir}/reports/vcftools/${meta.id}/${meta.variantcaller}/" }, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } diff --git a/tests/test_tools.yml b/tests/test_tools.yml index 6dd0e63c25..5412bf8e62 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -151,10 +151,10 @@ - germline - variant_calling files: - - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz - - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz.tbi - - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz - - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz.tbi + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on germline sample with deepvariant without intervals @@ -165,10 +165,10 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz - - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz.tbi - - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz - - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz.tbi + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz + - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on germline sample with freebayes @@ -178,8 +178,8 @@ - germline - variant_calling files: - - path: results/variant_calling/test/freebayes/test.vcf.gz - - path: results/variant_calling/test/freebayes/test.vcf.gz.tbi + - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz + - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on germline sample with freebayes without intervals @@ -190,8 +190,8 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/test/freebayes/test.vcf.gz - - path: results/variant_calling/test/freebayes/test.vcf.gz.tbi + - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz + - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with freebayes @@ -201,8 +201,8 @@ - somatic - variant_calling files: - - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz - - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz.tbi + - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz + - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with freebayes without intervals @@ -213,8 +213,8 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz - - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz.tbi + - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz + - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi - path: results/csv/variantcalled.csv # - name: Run variant calling on tumor_only sample with freebayes @@ -224,8 +224,8 @@ # - tumor_only # - variant_calling # files: -# - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz -# - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz.tbi +# - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz +# - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi # - name: Run variant calling on tumor_only sample with freebayes without intervals # command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools freebayes --no_intervals @@ -235,8 +235,8 @@ # - tumor_only # - variant_calling # files: -# - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz -# - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz.tbi +# - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz +# - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi - name: Run variant calling on germline sample with haplotypecaller command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller -c ./tests/nextflow.config --step variant_calling @@ -245,11 +245,15 @@ - haplotypecaller - variant_calling files: - - path: results/variant_calling/test/haplotypecaller/test.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test.vcf.gz.tbi - - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/csv/variantcalled.csv + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi - name: Run variant calling on germline sample with haplotypecaller without intervals command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller -c ./tests/nextflow.config --step variant_calling --no_intervals @@ -259,11 +263,15 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/test/haplotypecaller/test.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test.vcf.gz.tbi - - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/csv/variantcalled.csv + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi # - name: Run joint germline variant calling with haplotypecaller # command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline -c ./tests/nextflow.config @@ -273,10 +281,10 @@ # - haplotypecaller # - variant_calling # files: -# - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz -# - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz.tbi -# - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz -# - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz.tbi +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi # - path: results/csv/variantcalled.csv # - name: Run joint germline variant calling with haplotypecaller without intervals @@ -288,10 +296,10 @@ # - no_intervals # - variant_calling # files: -# - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz -# - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz.tbi -# - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz -# - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz.tbi +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz +# - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi # - path: results/csv/variantcalled.csv - name: Run variant calling on germline sample with manta @@ -301,8 +309,8 @@ - manta - variant_calling files: - - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz - - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi - name: Run variant calling on germline sample with manta without intervals command: nextflow run main.nf -profile test,tools_germline,docker --tools manta --no_intervals @@ -312,8 +320,8 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz - - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi - name: Run variant calling on tumor_only sample with manta command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta @@ -322,8 +330,8 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz - - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi + - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz + - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi - name: Run variant calling on tumor_only sample with manta without intervals command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta --no_intervals @@ -333,8 +341,8 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz - - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi + - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz + - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi - name: Run variant calling on somatic sample with manta command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta @@ -343,12 +351,12 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz - - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - name: Run variant calling on somatic sample with manta without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals @@ -358,12 +366,12 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz - - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - name: Run variant calling on tumor_only sample to test mpileup command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup @@ -406,16 +414,16 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.tbi - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.stats - - path: results/variant_calling/sample2/mutect2/sample2.contamination.table - - path: results/variant_calling/sample2/mutect2/sample2.segmentation.table - - path: results/variant_calling/sample2/mutect2/sample2.artifactprior.tar.gz - - path: results/variant_calling/sample2/mutect2/sample2.pileupsummaries.table - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.tbi - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.filteringStats.tsv + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv - path: results/csv/variantcalled.csv - name: Run variant calling on tumoronly sample with mutect2 without intervals @@ -426,16 +434,17 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.tbi - - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.stats - - path: results/variant_calling/sample2/mutect2/sample2.contamination.table - - path: results/variant_calling/sample2/mutect2/sample2.segmentation.table - - path: results/variant_calling/sample2/mutect2/sample2.artifactprior.tar.gz - - path: results/variant_calling/sample2/mutect2/sample2.pileupsummaries.table - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.tbi - - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.filteringStats.tsv + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileups.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi + - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with mutect2 @@ -446,17 +455,17 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with msisensor-pro @@ -478,10 +487,10 @@ - strelka - variant_calling files: - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on germline sample with strelka without intervals @@ -492,10 +501,10 @@ - no_intervals - variant_calling files: - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on tumoronly sample with strelka @@ -505,10 +514,10 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on tumoronly sample with strelka without intervals @@ -519,10 +528,10 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with strelka @@ -532,14 +541,14 @@ - strelka - variant_calling files: - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with strelka without intervals @@ -550,14 +559,14 @@ - strelka - variant_calling files: - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with strelka & manta (StrelkaBP) @@ -585,14 +594,20 @@ - strelkabp - variant_calling files: - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with tiddit @@ -602,15 +617,15 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample3/tiddit/sample3.ploidies.tab - - path: results/variant_calling/sample3/tiddit/sample3.vcf.gz - - path: results/variant_calling/sample3/tiddit/sample3.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.normal.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.normal.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tumor.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tumor.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3_sv_merge.vcf - - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.ploidies.tab + - path: results/variant_calling/sample3/tiddit/sample3.tiddit.ploidies.tab + - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz + - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit_sv_merge.vcf + - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.ploidies.tab - name: Run variant calling on germline sample with tiddit command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit -c ./tests/nextflow.config @@ -619,9 +634,9 @@ - germline - variant_calling files: - - path: results/variant_calling/sample1/tiddit/sample1.ploidies.tab - - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz - - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz.tbi + - path: results/variant_calling/sample1/tiddit/sample1.tiddit.ploidies.tab + - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz + - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz.tbi - name: Run variant calling on tumor_only sample with tiddit command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit -c ./tests/nextflow.config @@ -630,6 +645,6 @@ - tumor_only - variant_calling files: - - path: results/variant_calling/sample2/tiddit/sample2.ploidies.tab - - path: results/variant_calling/sample2/tiddit/sample2.vcf.gz - - path: results/variant_calling/sample2/tiddit/sample2.vcf.gz.tbi + - path: results/variant_calling/sample2/tiddit/sample2.tiddit.ploidies.tab + - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz + - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz.tbi diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 749d29c3ea..925b3ea3d5 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -32,15 +32,17 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileups.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileups.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv - path: results/csv/variantcalled.csv diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 72c7b71685..63bfbcac6b 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -761,7 +761,7 @@ workflow SAREK { }.set{convert} //BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format - BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai) + SAMTOOLS_BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai) ch_versions = ch_versions.mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.versions) cram_variant_calling = Channel.empty().mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.alignment_index, convert.cram) @@ -912,6 +912,7 @@ workflow SAREK { vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.manta_vcf) vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.strelka_vcf) vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.tiddit_vcf) + vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.freebayes_vcf) vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.mutect2_vcf) vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.manta_vcf) vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.strelka_vcf) @@ -923,7 +924,6 @@ workflow SAREK { ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions) //QC - vcf_to_annotate.dump(tag:'vcf_to_annotate') VCF_QC(vcf_to_annotate, intervals_bed_combined) ch_versions = ch_versions.mix(VCF_QC.out.versions) @@ -976,8 +976,6 @@ workflow SAREK { ch_reports.collect() ) - ch_multiqc_files.view() - MULTIQC(ch_multiqc_files.collect(), ch_multiqc_config) multiqc_report = MULTIQC.out.report.toList() } From 2c2cbdbe0442aa79a0d2913f2a9333f8c2b679cb Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 13 Jul 2022 12:00:59 +0000 Subject: [PATCH 06/13] update ymls --- tests/test_default.yml | 8 +++---- tests/test_markduplicates.yml | 16 +++++++------- tests/test_prepare_recalibration.yml | 32 ++++++++++++++-------------- tests/test_recalibrate.yml | 32 ++++++++++++++-------------- tests/test_skip_markduplicates.yml | 24 ++++++++++----------- tests/test_tools.yml | 14 ++++++++---- 6 files changed, 66 insertions(+), 60 deletions(-) diff --git a/tests/test_default.yml b/tests/test_default.yml index 03eda15635..8dc3ed2c5c 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -82,7 +82,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.md.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml index 7c9c459c85..8760496ebb 100644 --- a/tests/test_markduplicates.yml +++ b/tests/test_markduplicates.yml @@ -24,10 +24,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.md.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Mark Duplicates starting from CRAM command: nextflow run main.nf -profile test,markduplicates_cram,docker --tools strelka @@ -55,7 +55,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.md.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml index d6e0b4a752..2dd54b74e9 100644 --- a/tests/test_prepare_recalibration.yml +++ b/tests/test_prepare_recalibration.yml @@ -15,10 +15,10 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Prepare_recal starting from cram command: nextflow run main.nf -profile test,prepare_recalibration_cram,docker --tools strelka @@ -37,10 +37,10 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Prepare_recal starting from bam and skip baserecalibration command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr,docker --tools strelka @@ -70,10 +70,10 @@ should_exist: false - path: results/reports/samtools_stats/test/test.recal.cram.stats should_exist: false - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Prepare_recal starting from cram and skip baserecalibration command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr,docker --tools strelka @@ -105,7 +105,7 @@ should_exist: false - path: results/reports/samtools_stats/test/test.recal.cram.stats should_exist: false - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml index 47b470a00f..d62ab2662a 100644 --- a/tests/test_recalibrate.yml +++ b/tests/test_recalibrate.yml @@ -14,10 +14,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.recal.cram.stats - path: results/csv/recalibrated.csv - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Recalibration starting from cram command: nextflow run main.nf -profile test,recalibrate_cram,docker --tools strelka @@ -35,10 +35,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.recal.cram.stats - path: results/csv/recalibrated.csv - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Recalibration starting from bam and skip baserecalibration command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr,docker --tools strelka @@ -68,10 +68,10 @@ should_exist: false - path: results/reports/samtools_stats/test/test.recal.cram.stats should_exist: false - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run Recalibration starting from cram and skip baserecalibration command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr,docker --tools strelka @@ -103,7 +103,7 @@ should_exist: false - path: results/reports/samtools_stats/test/test.recal.cram.stats should_exist: false - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index ef5ef221f7..047ebb89f8 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -26,10 +26,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.md.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run skip markduplicates bam from step markduplicates command: nextflow run main.nf -profile test,docker,markduplicates_bam,skip_markduplicates --tools strelka @@ -57,10 +57,10 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.md.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi - name: Run skip markduplicates cram from step markduplicates command: nextflow run main.nf -profile test,docker,markduplicates_cram,skip_markduplicates --tools strelka @@ -92,7 +92,7 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - path: results/reports/samtools_stats/test/test.paired_end.sorted.cram.stats - path: results/reports/samtools_stats/test/test.recal.cram.stats - - path: results/variant_calling/test/strelka/test.genome.vcf.gz - - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi - - path: results/variant_calling/test/strelka/test.variants.vcf.gz - - path: results/variant_calling/test/strelka/test.variants.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz + - path: results/variant_calling/test/strelka/test.strelka.variants.vcf.gz.tbi diff --git a/tests/test_tools.yml b/tests/test_tools.yml index 5412bf8e62..270b8a0623 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -576,10 +576,16 @@ - strelkabp - variant_calling files: - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi + - path: results/variant_calling/sample3/manta/sample3.manta.variants.vcf.gz + - path: results/variant_calling/sample3/manta/sample3.manta.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi + - path: results//variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz + - path: results//variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi + - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz + - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi + - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz + - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz From a4b21dc1347d9ef67d96a2f5dfd84ebc4a356956 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 13 Jul 2022 12:45:00 +0000 Subject: [PATCH 07/13] update ymls --- tests/test_only_paired_VC.yml | 64 +++++++++++++++++------------------ tests/test_tools.yml | 16 ++++----- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index 2c2dcae353..143c2731c7 100644 --- a/tests/test_only_paired_VC.yml +++ b/tests/test_only_paired_VC.yml @@ -27,26 +27,26 @@ - strelka - variantcalling_channel files: - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz should_exist: false - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi should_exist: false - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz should_exist: false - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi should_exist: false - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - name: Do germline variant calling on matched normal command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka @@ -55,19 +55,19 @@ - strelka - variantcalling_channel files: - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz - - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz - - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz - - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi diff --git a/tests/test_tools.yml b/tests/test_tools.yml index 270b8a0623..db23ecbe6b 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -250,10 +250,10 @@ - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/csv/variantcalled.csv - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi - name: Run variant calling on germline sample with haplotypecaller without intervals command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller -c ./tests/nextflow.config --step variant_calling --no_intervals @@ -268,10 +268,10 @@ - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi - path: results/csv/variantcalled.csv - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz - - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz + - path: results/variant_calling/test1/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi # - name: Run joint germline variant calling with haplotypecaller # command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline -c ./tests/nextflow.config From 2f966b44d82c5e06d26766ea897565c0e9ddb80c Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 13 Jul 2022 13:45:24 +0000 Subject: [PATCH 08/13] update yml --- tests/test_tools.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_tools.yml b/tests/test_tools.yml index db23ecbe6b..60ed11f5b9 100644 --- a/tests/test_tools.yml +++ b/tests/test_tools.yml @@ -576,8 +576,8 @@ - strelkabp - variant_calling files: - - path: results/variant_calling/sample3/manta/sample3.manta.variants.vcf.gz - - path: results/variant_calling/sample3/manta/sample3.manta.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz + - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi - path: results//variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz @@ -586,10 +586,10 @@ - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz - path: results//variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - path: results/csv/variantcalled.csv - name: Run variant calling on somatic sample with & manta (StrelkaBP) without intervals From 1992894fd32c5e43420b3c7645f19e5be98fc939 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Wed, 13 Jul 2022 14:01:19 +0000 Subject: [PATCH 09/13] update ascat yml --- tests/test_tools_manually.yml | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 925b3ea3d5..9d1a49dcaa 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -6,22 +6,20 @@ - somatic - variant_calling files: - - path: results/variant_calling/sample4_vs_sample3/ascat/After_correction_GC_Tumour.germline.png - - path: results/variant_calling/sample4_vs_sample3/ascat/After_correction_GC_Tumour.tumour.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Before_correction_Tumour.germline.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Before_correction_Tumour.tumour.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Normal_alleleFrequencies_chr21.txt - - path: results/variant_calling/sample4_vs_sample3/ascat/Normal_alleleFrequencies_chr22.txt + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.germline.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.after_correction_gc_rt.sample4_vs_sample3.tumour.tumour.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.germline.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.before_correction.sample4_vs_sample3.tumour.tumour.png - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.cnvs.txt - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.metrics.txt - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.purityploidy.txt - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.segments.txt - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour_alleleFrequencies_chr21.txt - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour_alleleFrequencies_chr22.txt - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.ASCATprofile.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.ASPCF.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.rawprofile.png - - path: results/variant_calling/sample4_vs_sample3/ascat/Tumour.sunrise.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour.ASPCF.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_normalBAF.txt + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_normalLogR.txt + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour.sunrise.png + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_tumourBAF.txt + - path: results/variant_calling/sample4_vs_sample3/ascat/sample4_vs_sample3.tumour_tumourLogR.txt - name: Run variant calling on somatic sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 --no_intervals -c ./tests/nextflow.config From 4a5ed754d440f55195f45574e2436e9f4ff881f7 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Thu, 14 Jul 2022 06:32:09 +0000 Subject: [PATCH 10/13] add suggested changes + rm view/dumps --- CHANGELOG.md | 5 +++++ conf/modules.config | 30 ++++++++++++++++-------------- workflows/sarek.nf | 3 --- 3 files changed, 21 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b2a249819a..b3b9fab5ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -81,6 +81,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#608](https://github.com/nf-core/sarek/pull/608) - Prevent candidate VCFs from getting published in manta - [#620](https://github.com/nf-core/sarek/pull/620) - `gender` is now `sex` in the samplesheet - [#630](https://github.com/nf-core/sarek/pull/630) - Update citations file +- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files +- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files ### Fixed @@ -122,6 +124,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#619](https://github.com/nf-core/sarek/pull/619) - Fix issue with checking samplesheet content with AWS - [#628](https://github.com/nf-core/sarek/pull/628) - Fix issue with value converting to string before schema validation - [#628](https://github.com/nf-core/sarek/pull/628) - Fix dbsnp check issue with `--step annotate` +- [#618](https://github.com/nf-core/sarek/pull/618) - Fix `bcftools/vcftools` sample labelling in multiqc report +- [#618](https://github.com/nf-core/sarek/pull/618) - Fix issue with tiddit [#621](https://github.com/nf-core/sarek/issues/621) +- [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals ### Deprecated diff --git a/conf/modules.config b/conf/modules.config index 0e9e3e8942..bbae740dd6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1084,23 +1084,25 @@ process{ ext.prefix = {"${meta.id}.strelka.somatic_snvs"} } + if (params.tools && params.tools.contains('tiddit')) { //TIDDIT - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.tiddit.normal.vcf"} - } + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { + ext.prefix = {"${meta.id}.tiddit.normal.vcf"} + } - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.tiddit.tumor.vcf"} - } + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { + ext.prefix = {"${meta.id}.tiddit.tumor.vcf"} + } - //SVDB - withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' { - ext.prefix = { "${meta.id}.tiddit" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }, - pattern: "*vcf" - ] + //SVDB + withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' { + ext.prefix = { "${meta.id}.tiddit" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" }, + pattern: "*vcf" + ] + } } // VCF QC diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 9e26ee64bc..f06013a36f 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -871,8 +871,6 @@ workflow SAREK { pon_tbi ) - //intervals_bed_combined.dump(tag:'intervals before pair variant calling') - //PREPARE_INTERVALS.out.intervals_bed_combined.dump(tag:'intervals before pair variant calling PREPARE INTERVALS:OUT') // PAIR VARIANT CALLING PAIR_VARIANT_CALLING( params.tools, @@ -957,7 +955,6 @@ workflow SAREK { } } - ch_reports.collect().dump(tag:'ch_reports2') ch_version_yaml = Channel.empty() if (!(params.skip_tools && params.skip_tools.contains('versions'))) { From e750e4ecc68f9b604c7bdf66a516bbd31865b65a Mon Sep 17 00:00:00 2001 From: SusiJo Date: Thu, 14 Jul 2022 07:24:28 +0000 Subject: [PATCH 11/13] revert back to former multiqc_config --- assets/multiqc_config.yml | 47 ++++++--------------------------------- 1 file changed, 7 insertions(+), 40 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 28e60a1f6c..6b6fdb1c7f 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -6,6 +6,11 @@ report_comment: > This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation. +report_section_order: + software_versions: + order: -1000 + nf-core-sarek-summary: + order: -1001 export_plots: true @@ -34,33 +39,9 @@ module_order: name: "GATK4 MarkDuplicates" info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)." - samtools: - name: "Samtools Flagstat (mapped)" - fn: "*.md.cram.stats" - anchor: "md_stats" - info: "This section of the report shows mapped samtools stats." - path_filters: - - "*.md.cram.stats" - - mosdepth: - name: "Mosdepth (mapped)" - fn: "*.mapped.mosdepth.*.dist.txt" - anchor: "mapped_mosdepth" - info: "This section of the report shows the mapped distribution after mosdepth." - path_filters: - - "*.mapped.mosdepth.*.dist.txt" - - samtools: - name: "Samtools Flagstat (recal)" - fn: "*.recal.cram.stats" - anchor: "recal_stats" - info: "This section of the report shows recalibrated samtools stats." - path_filters: - - "*.recal.cram.stats" + name: "Samtools Flagstat" - mosdepth: - name: "Mosdepth (recalibrated)" - fn: "*.recal.mosdepth.*.dist.txt" - anchor: "recal_mosdepth" - info: "This section of the report shows the recalibrated distribution after mosdepth." - path_filters: - - "*.recal.mosdepth.*.dist.txt" + name: "Mosdepth" - gatk: name: "GATK4 BQSR" - bcftools: @@ -72,23 +53,9 @@ module_order: - vep: name: "VEP" -report_section_order: - md_stats: - before: recal_stats - mapped_mosdepth: - before: recal_mosdepth - software_versions: - order: -1000 - nf-core-sarek-summary: - order: -1001 - extra_fn_clean_exts: - "_val" -#fn_clean_sample_names: false - -#use_filename_as_sample_name: true - sp: snpeff: contents: "SnpEff_version" From 558ecd3827d198ff534ed817ce894baab73dbca1 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Thu, 14 Jul 2022 07:39:41 +0000 Subject: [PATCH 12/13] add description schema description for ascat --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 1b10439d51..8d94a9b986 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -454,6 +454,7 @@ }, "ascat_chromosomes": { "type": "string", + "description": "Chromosomes to run ASCAT on.", "fa_icon": "fa-solid fa-text", "default": "c(1:22, 'X')", "help_text": "Specify specific chromosomes to run ASCAT on, i.e 'c('21', '22')'." From 43a0a52ad09322f018746d81ae6d2c2e30c78002 Mon Sep 17 00:00:00 2001 From: SusiJo Date: Thu, 14 Jul 2022 08:22:15 +0000 Subject: [PATCH 13/13] rm unnecessary ext.args for multiqc --- conf/modules.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 90e1d2b37c..8ba1e84768 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1219,7 +1219,5 @@ process{ // MULTIQC withName:'MULTIQC' { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} - //ext.args = { params.multiqc_config ? "--config $multiqc_custom_config" : "" } - //ext.args = '-d' } }