# assets/output_contract.tsv: what OwnGenome 1.0 keeps stable (docs/output-contract.md). # scripts/ci/check-output-contract.py reads it: --static in Guard's unit-tests job (tests/test_output_contract.py) # checks every row against the code, and the e2e case output-contract-1-hg002 checks the files the # HG002 run wrote. Columns, tab-separated: # kind file, param (a nextflow_schema.json param), tool (a --tools name in main.nf) or # switch (a run-all.sh switch, its SWITCHES list) # name file: its path under the results folder (GENOME_DIR for the bash steps and run-all.sh, # --outdir for nextflow run), {sample} for the sample id, {family} for --family_name; # * where the name varies. Other kinds: the name as typed. # step the step number (assets/steps.tsv), - for none # process the Nextflow process that publishes the file, - when no module does (a bash step, # run-all.sh or main.nf itself) # legs file: who writes it under this name: nextflow (main.nf and run-all.sh), bash (the # single step script), both. Other kinds: - # format file: tsv, csv, vcf, json, text, html, bam, cram, index, bed, dir, zip, svg, png, md, # yml, fasta, bin. Other kinds: - # stability stable: kept until 2.0; experimental: an opt-in engine new in 1.0, listed but free to # change in a 1.x release; internal: a task file that is not published, listed so the # list stays complete # e2e the leg (bash, nextflow, both) whose HG002 e2e run must write the file, - for none # required tsv and csv: the columns; vcf: the INFO/ and FORMAT/ fields of its header; json: the # top-level keys; comma-separated, - for none. More columns may come; none of these may go. kind name step process legs format stability e2e required file multiqc/multiqc_report.html 28 MULTIQC nextflow html stable - - file multiqc/multiqc_report_data 28 MULTIQC nextflow dir stable - - file pipeline_info/software_versions.yml - - nextflow yml stable nextflow - file somalier/somalier.html 33 SOMALIER_RELATE nextflow html experimental - - file somalier/somalier.pairs.tsv 33 SOMALIER_RELATE nextflow tsv experimental - - file somalier/somalier.samples.tsv 33 SOMALIER_RELATE nextflow tsv experimental - - file {family}/compound_het.tsv 38 FAMILY_REPORT nextflow tsv experimental - - file {family}/couple_*.md 39 COUPLE_CARRIER nextflow md experimental - - file {family}/couple_*.tsv 39 COUPLE_CARRIER nextflow tsv experimental - - file {family}/de_novo.tsv 38 FAMILY_REPORT nextflow tsv experimental - - file {family}/family.ped 38 FAMILY_PREPARE nextflow tsv experimental - - file {family}/family.phased.vcf.gz 38 WHATSHAP_PED nextflow vcf experimental - - file {family}/family.phased.vcf.gz.tbi 38 WHATSHAP_PED nextflow index experimental - - file {family}/family.vcf.gz 38 GLNEXUS_VCF nextflow vcf experimental - - file {family}/family.vcf.gz.tbi 38 GLNEXUS_VCF nextflow index experimental - - file {family}/family_plan.tsv 38 FAMILY_PREPARE nextflow tsv experimental - - file {family}/family_report.md 38 FAMILY_REPORT nextflow md experimental - - file {family}/ibd_pairs.tsv 38 FAMILY_IBD_REPORT nextflow tsv experimental - - file {family}/ibd_report.md 38 FAMILY_IBD_REPORT nextflow md experimental - - file {family}/ibd_segments.tsv 38 FAMILY_IBD_REPORT nextflow tsv experimental - - file {family}/members.tsv 38 FAMILY_PREPARE nextflow tsv experimental - - file {family}/pedigree.tsv 38 FAMILY_PREPARE nextflow tsv experimental - - file {family}/relationships.tsv 38 FAMILY_CHECK nextflow tsv experimental - - file {family}/somalier/family.html 38 FAMILY_RELATE nextflow html experimental - - file {family}/somalier/family.pairs.tsv 38 FAMILY_RELATE nextflow tsv experimental - - file {family}/somalier/family.samples.tsv 38 FAMILY_RELATE nextflow tsv experimental - - file {family}/trios.ped 38 FAMILY_PREPARE nextflow tsv experimental - - file {family}/{sample}_dnapainter.csv 38 FAMILY_REPORT nextflow csv experimental - - file {family}/{sample}_inheritance.tsv.gz 38 FAMILY_REPORT nextflow tsv experimental - - file {family}/{sample}_segments.svg 38 FAMILY_REPORT nextflow svg experimental - - file {family}/{sample}_segments.tsv 38 FAMILY_REPORT nextflow tsv experimental - - file {sample}/aligned/{sample}_sorted.bam 02 ALIGN_MINIMAP2 both bam stable bash - file {sample}/aligned/{sample}_sorted.bam.bai 02 ALIGN_MINIMAP2 both index stable bash - file {sample}/aligned/{sample}_sorted.cram 34 CRAM_ARCHIVE both cram experimental - - file {sample}/aligned/{sample}_sorted.cram.crai 34 CRAM_ARCHIVE both index experimental - - file {sample}/aligned/{sample}_sorted.cram.flagstat 34 CRAM_ARCHIVE both bin experimental - - file {sample}/ancestry/{sample}_ancestry.tsv 25 PRS_SUMMARY both tsv stable - - file {sample}/ancestry_fine/{sample}_ancestry_fine.tsv 26b ANCESTRY_FINE_REPORT both tsv experimental - - file {sample}/ancestry_fine/{sample}_ancestry_fine.txt 26b ANCESTRY_FINE_REPORT nextflow text experimental - - file {sample}/ancestry_fine/{sample}_painting.bed 26b ANCESTRY_FINE_REPORT both bed experimental - - file {sample}/ancestry_fine/{sample}_painting.png 26b ANCESTRY_FINE_REPORT both png experimental - - file {sample}/ancient/{sample}_ancient.tsv 44 ANCIENT_REPORT both tsv experimental - - file {sample}/ancient/{sample}_ancient.txt 44 ANCIENT_REPORT both text experimental - - file {sample}/ancient/{sample}_ancient_info.tsv 44 ANCIENT_REPORT both tsv experimental - - file {sample}/ancient/{sample}_ancient_pca.svg 44 ANCIENT_REPORT both svg experimental - - file {sample}/annotsv/{sample}_annotsv_input.vcf 05 ANNOTSV both vcf stable - - file {sample}/annotsv/{sample}_sv_annotated.tsv 05 ANNOTSV both tsv stable - - file {sample}/annotsv/{sample}_sv_class4_5.tsv 05 ANNOTSV both tsv stable - - file {sample}/annotsv/{sample}_sv_class4_5_checked.tsv 05 ANNOTSV both tsv stable - - file {sample}/archaic/{sample}_archaic.tsv 43 ARCHAIC_REPORT both tsv experimental - - file {sample}/archaic/{sample}_archaic.txt 43 ARCHAIC_REPORT both text experimental - - file {sample}/archaic/{sample}_archaic_segments.tsv 43 ARCHAIC_REPORT both tsv experimental - - file {sample}/bloodtype/{sample}_bloodtype.tsv 41 BLOODTYPE both tsv experimental - - file {sample}/bloodtype/{sample}_bloodtype_depth.tsv 41 BLOODTYPE_DEPTH both tsv experimental - - file {sample}/bloodtype/{sample}_bloodtype_evidence.tsv 41 BLOODTYPE both tsv experimental - - file {sample}/chip/{sample}_chip.tsv 49 CHIP_REPORT both tsv experimental - - file {sample}/chip/{sample}_chip_depth.tsv 49 CHIP_REPORT both tsv experimental - - file {sample}/chip/{sample}_chip_filtered.vcf.gz 49 CHIP_MUTECT2 both vcf experimental - - file {sample}/clinical/{sample}_clinical.vcf.gz 23 CLINICAL_FILTER both vcf stable bash - file {sample}/clinical/{sample}_clinical.vcf.gz.tbi 23 CLINICAL_FILTER nextflow index stable - - file {sample}/clinical/{sample}_clinical_summary.tsv 23 CLINICAL_FILTER both tsv stable - - file {sample}/clinvar/{sample}_clinvar_cdna_check.tsv 06 CLINVAR_CDNA_CHECK both tsv stable - - file {sample}/clinvar/{sample}_clinvar_cdna_scan.tsv 06 CLINVAR_CDNA_CHECK both tsv stable - - file {sample}/clinvar/{sample}_clinvar_deep_intronic.tsv 06 CLINVAR_SCREEN both tsv stable - - file {sample}/clinvar/{sample}_clinvar_hits.tsv 06 CLINVAR_SCREEN both tsv stable both chrom,pos,ref,alt,genotype,clinvar_id,geneinfo,clnsig,clnrevstat file {sample}/clinvar/{sample}_clinvar_hits.vcf 06 CLINVAR_SCREEN both vcf stable both INFO/GENEINFO,INFO/CLNSIG,INFO/CLNREVSTAT file {sample}/clinvar/{sample}_pass.vcf.gz 06 CLINVAR_SCREEN both vcf stable both FORMAT/GT file {sample}/clinvar/{sample}_pass.vcf.gz.tbi 06 CLINVAR_SCREEN both index stable both - file {sample}/cnvpytor/{sample}_cnvs.raw.vcf 18 CNVPYTOR nextflow vcf internal - - file {sample}/cnvpytor/{sample}_cnvs.txt 18 CNVPYTOR both text stable - - file {sample}/cnvpytor/{sample}_cnvs.vcf.gz 18 CNVPYTOR_VCF both vcf stable - - file {sample}/cnvpytor/{sample}_cnvs.vcf.gz.tbi 18 CNVPYTOR_VCF nextflow index stable - - file {sample}/consumer_export/{sample}_23andme_v5.zip 40 CONSUMER_EXPORT both zip experimental - - file {sample}/consumer_export/{sample}_ancestrydna_layout.zip 40 CONSUMER_EXPORT both zip experimental - - file {sample}/consumer_export/{sample}_consumer_export.tsv 40 CONSUMER_EXPORT both tsv experimental - - file {sample}/couple/{sample}_couple_carrier.tsv 39 COUPLE_CARRIER both tsv experimental - - file {sample}/coverage/{sample}.mosdepth.global.dist.txt 16b MOSDEPTH nextflow text stable - - file {sample}/coverage/{sample}.mosdepth.summary.txt 16b MOSDEPTH nextflow tsv stable nextflow chrom,length,bases,mean,min,max file {sample}/coverage/{sample}.regions.bed.gz 16b MOSDEPTH nextflow bed stable - - file {sample}/coverage/{sample}.thresholds.bed.gz 16b MOSDEPTH nextflow bed stable - - file {sample}/coverage/{sample}_callability.bed.gz 16b MOSDEPTH nextflow bed stable - - file {sample}/cpic/{sample}_cpic_recommendations.txt 27 CPIC_LOOKUP both text stable both - file {sample}/cpic/{sample}_phenotypes.tsv 27 CPIC_LOOKUP both tsv stable both - file {sample}/cpsr/{sample}.cpsr.grch38.classification.tsv.gz 17 CPSR both tsv stable - - file {sample}/cpsr/{sample}.cpsr.grch38.html 17 CPSR both html stable - - file {sample}/cpsr/{sample}_cpsr_cdna_check.tsv 17 CLINVAR_CDNA_CHECK both tsv stable - - file {sample}/cyrius/{sample}_cyp2d6.tsv 21 CYRIUS both tsv stable - - file {sample}/cyrius/{sample}_cyp2d6_depth_check.tsv 21 CYRIUS both tsv stable - - file {sample}/delly/{sample}_sv.vcf.gz 19 DELLY_BCF2VCF both vcf stable nextflow INFO/SVTYPE file {sample}/delly/{sample}_sv.vcf.gz.tbi 19 DELLY_BCF2VCF nextflow index stable nextflow - file {sample}/exomiser/{sample}_exomiser.txt 48 EXOMISER_REPORT both text experimental - - file {sample}/exomiser/{sample}_exomiser.variants.tsv 48 EXOMISER both tsv experimental - - file {sample}/exomiser/{sample}_exomiser_terms.tsv 48 EXOMISER_REPORT both tsv experimental - - file {sample}/exomiser/{sample}_exomiser_top.tsv 48 EXOMISER_REPORT both tsv experimental - - file {sample}/expansion_hunter/{sample}.json 09 EXPANSION_HUNTER nextflow json stable - - file {sample}/expansion_hunter/{sample}.vcf 09 EXPANSION_HUNTER nextflow vcf stable - - file {sample}/expansion_hunter/{sample}_eh_stranger.vcf 09b STRANGER both vcf stable - - file {sample}/expansion_hunter/{sample}_realigned.bam 09 EXPANSION_HUNTER nextflow bam stable - - file {sample}/expansion_hunter/{sample}_rfc1_motif.tsv 09b STRANGER_RFC1 both tsv stable - - file {sample}/expansion_hunter/{sample}_str_motifs.tsv 09b STRANGER_RFC1 both tsv stable - - file {sample}/fastq_trimmed/{sample}_R1.fastq.gz 01b FASTP nextflow bin internal - - file {sample}/fastq_trimmed/{sample}_R2.fastq.gz 01b FASTP nextflow bin internal - - file {sample}/fastq_trimmed/{sample}_fastp.html 01b FASTP both html stable - - file {sample}/fastq_trimmed/{sample}_fastp.json 01b FASTP both json stable - - file {sample}/hla/{sample}_hla_genotype.tsv 08 HLA_TYPING nextflow tsv stable - - file {sample}/hla_optitype/{sample}_hla_concordance.tsv 08 HLA_QC both tsv experimental - - file {sample}/hla_optitype/{sample}_optitype_result.tsv 08 HLA_QC both tsv experimental - - file {sample}/hla_t1k/{sample}_hla_genotype.tsv 08 - bash tsv stable bash - file {sample}/indexcov 16 INDEXCOV both dir stable - - file {sample}/indexcov/indexcov-indexcov.ped 16 - bash tsv stable bash - file {sample}/kir/database_release.txt 08 KIR_TYPING nextflow text experimental - - file {sample}/kir/{sample}_kir_genotype.tsv 08 KIR_TYPING both tsv experimental - - file {sample}/logs/run_status.tsv - - nextflow tsv stable - - file {sample}/lpa/{sample}_lpa_kiv2.tsv 46 LPA both tsv experimental - - file {sample}/lpa/{sample}_lpa_kiv2_depth.tsv 46 LPA_DEPTH both tsv experimental - - file {sample}/lpa/{sample}_lpa_kiv2_depth_q1.tsv 46 LPA_DEPTH both tsv experimental - - file {sample}/manta/results/variants/candidateSV.vcf.gz 04 MANTA both vcf stable - - file {sample}/manta/results/variants/diploidSV.raw.vcf.gz 04 MANTA both vcf stable - - file {sample}/manta/results/variants/diploidSV.raw.vcf.gz.tbi 04 MANTA both index stable - - file {sample}/manta/results/variants/diploidSV.vcf.gz 04 MANTA both vcf stable - - file {sample}/manta/results/variants/diploidSV.vcf.gz.tbi 04 MANTA both index stable - - file {sample}/mei/{sample}_megane.log 50 MEI both text experimental - - file {sample}/mei/{sample}_megane.vcf 50 MEI both vcf experimental - - file {sample}/mei/{sample}_mei.tsv 50 MEI_REPORT both tsv experimental - - file {sample}/mei/{sample}_mei_annotsv.tsv 50 MEI_REPORT both tsv experimental - - file {sample}/mei/{sample}_mei_depth.tsv 50 MEI_DEPTH both tsv experimental - - file {sample}/mei/{sample}_mei_mainchr.txt 50 MEI_DEPTH nextflow text internal - - file {sample}/mei/{sample}_mei_sites.tsv 50 MEI_REPORT both tsv experimental - - file {sample}/mito/{sample}_chrM.fasta 12 MITO_EXTRACT_CHRM both fasta stable - - file {sample}/mito/{sample}_chrM.vcf.gz 12 MITO_EXTRACT_CHRM nextflow vcf internal - - file {sample}/mito/{sample}_chrM.vcf.gz.tbi 12 MITO_EXTRACT_CHRM nextflow index internal - - file {sample}/mito/{sample}_chrM_annotated.tsv 20 MITO_VARIANTS_ANNOTATE both tsv stable - - file {sample}/mito/{sample}_chrM_deletions.tsv 20 MITO_DELETIONS both tsv stable - - file {sample}/mito/{sample}_chrM_filtered.vcf.gz 20 MITO_VARIANTS both vcf stable bash - file {sample}/mito/{sample}_chrM_filtered.vcf.gz.tbi 20 MITO_VARIANTS nextflow index stable - - file {sample}/mito/{sample}_chrM_mutect2.vcf.gz.stats 20 MITO_VARIANTS nextflow bin stable - - file {sample}/mito/{sample}_haplocheck.txt 12 HAPLOCHECK both text stable - - file {sample}/mito/{sample}_haplogroup.txt 12 MITO_HAPLOGROUP both text stable bash - file {sample}/mito/{sample}_mtdna_copies.tsv 20 MITO_DELETIONS both tsv stable - - file {sample}/mosaic/{sample}_mocha.log 51 MOCHA_CALL both text experimental - - file {sample}/mosaic/{sample}_mocha.tsv 51 MOCHA_REPORT both tsv experimental - - file {sample}/mosaic/{sample}_mocha_calls_raw.tsv 51 MOCHA_CALL both tsv experimental - - file {sample}/mosaic/{sample}_mocha_sites.tsv 51 MOCHA_CALL both tsv experimental - - file {sample}/mosaic/{sample}_mocha_stats.tsv 51 MOCHA_CALL both tsv experimental - - file {sample}/mosaic/{sample}_mocha_summary.tsv 51 MOCHA_REPORT both tsv experimental - - file {sample}/locityper/{sample}_locityper.log 53 LOCITYPER both text experimental - - file {sample}/locityper/{sample}_locityper.tsv 53 LOCITYPER both tsv experimental - - file {sample}/locityper/work 53 LOCITYPER both dir experimental - - file {sample}/mosdepth/{sample}.mosdepth.summary.txt 16b - bash tsv stable bash chrom,length,bases,mean,min,max file {sample}/paralogs/{sample}_*_copy_number.tsv 35 PARASCOPY both tsv experimental - - file {sample}/paralogs/{sample}_cn_dosage.tsv 35 PARASCOPY both tsv experimental - - file {sample}/paralogs/{sample}_cn_intervals.tsv 35 PARASCOPY both tsv experimental - - file {sample}/paralogs/{sample}_cyp21a2_psv.tsv 35 PARASCOPY both tsv experimental - - file {sample}/paralogs/{sample}_hba_copy_number.tsv 35 PARASCOPY both tsv experimental - - file {sample}/paralogs/{sample}_paraphase 35b PARAPHASE both dir experimental - - file {sample}/paralogs/{sample}_paraphase_copy_number.tsv 35b PARAPHASE_REPORT both tsv experimental - - file {sample}/paralogs/{sample}_paraphase_variants.tsv 35b PARAPHASE_REPORT both tsv experimental - - file {sample}/paralogs/{sample}_parascopy 35 PARASCOPY both dir experimental - - file {sample}/paralogs/{sample}_smn_copy_number.tsv 35 PARASCOPY both tsv experimental - - file {sample}/pgx_consensus/{sample}_outside_calls.tsv 36 PGX_CONSENSUS both tsv stable - - file {sample}/pgx_consensus/{sample}_pgx_consensus.tsv 36 PGX_CONSENSUS both tsv stable - - file {sample}/pharmcat/{sample}.match.json 07 PHARMCAT nextflow json stable - - file {sample}/pharmcat/{sample}.phenotype.json 07 PHARMCAT nextflow json stable - - file {sample}/pharmcat/{sample}.report.html 07 PHARMCAT nextflow html stable - - file {sample}/pharmcat/{sample}.report.json 07 PHARMCAT nextflow json stable nextflow - file {sample}/prs/pgsc_calc 25 PRS both dir stable - - file {sample}/prs/{sample}_prs_summary.*.tsv 25 PRS_SUMMARY nextflow tsv stable - - file {sample}/prs/{sample}_prs_summary.tsv 25 PRS_SUMMARY both tsv stable - - file {sample}/pypgx/{sample}_cyp2d6_depth_check.tsv 32 PYPGX both tsv stable - - file {sample}/pypgx/{sample}_pharmcat_comparison.tsv 27 CPIC_LOOKUP both tsv stable - - file {sample}/pypgx/{sample}_pypgx_results 32 PYPGX nextflow dir stable - - file {sample}/pypgx/{sample}_pypgx_summary.tsv 32 PYPGX both tsv stable bash - file {sample}/qc/somalier/{sample}.somalier 33 SOMALIER nextflow bin experimental - - file {sample}/qc/somalier/{sample}.somalier_id 33 SOMALIER nextflow bin internal - - file {sample}/qc/verifybamid2/{sample}.Ancestry 33 VERIFYBAMID2 nextflow bin experimental - - file {sample}/qc/verifybamid2/{sample}.log 33 VERIFYBAMID2 both text experimental - - file {sample}/qc/verifybamid2/{sample}.marker_check 33 VERIFYBAMID2 nextflow bin internal - - file {sample}/qc/verifybamid2/{sample}.selfSM 33 VERIFYBAMID2 both bin experimental - - file {sample}/qc/{sample}_read_count.tsv 02 ALIGN_MINIMAP2 both tsv stable - - file {sample}/qc/{sample}_sample_qc.tsv 33 SAMPLE_QC both tsv experimental - - file {sample}/roh/{sample}_roh.txt 11 ROH nextflow text stable nextflow - file {sample}/roh/{sample}_roh_summary.txt 11 ROH nextflow tsv stable nextflow chrom,start,end,length_bp,length_mb file {sample}/run_manifest.tsv - - nextflow tsv stable - - file {sample}/slivar/{sample}.ped 31 SLIVAR_PRIORITIZE nextflow tsv internal - - file {sample}/slivar/{sample}_compound_het_pairs.tsv 31 COMPHET_PHASE both tsv stable - - file {sample}/slivar/{sample}_compound_hets.vcf.gz 31 SLIVAR both vcf stable bash - file {sample}/slivar/{sample}_prioritized.vcf.gz 31 SLIVAR_PRIORITIZE both vcf stable bash - file {sample}/slivar/{sample}_prioritized.vcf.gz.tbi 31 SLIVAR_PRIORITIZE nextflow index stable - - file {sample}/slivar/{sample}_slivar_summary.tsv 31 SLIVAR_PRIORITIZE both tsv stable - - file {sample}/summary.json 24 HTML_REPORT both json stable bash schema_version,sample,generated_utc,run,databases,manifest,sections,cyp2d6,not_run,not_assessed file {sample}/sv_duphold/{sample}_sv_duphold.vcf 15 DUPHOLD nextflow vcf stable - - file {sample}/sv_filtered/{sample}_sv_filtered.log 15 DUPHOLD_FILTER nextflow text stable - - file {sample}/sv_filtered/{sample}_sv_filtered.vcf.gz 15 DUPHOLD_FILTER nextflow vcf stable - - file {sample}/sv_filtered/{sample}_sv_filtered.vcf.gz.tbi 15 DUPHOLD_FILTER nextflow index stable - - file {sample}/sv_merged/{sample}_sv_consensus.vcf.gz 22 SURVIVOR_SORT both vcf stable - - file {sample}/sv_merged/{sample}_sv_consensus.vcf.gz.tbi 22 SURVIVOR_SORT both index stable - - file {sample}/telomere/{sample} 10 TELOMERE_HUNTER both dir stable - - file {sample}/traits/{sample}_genotype_rules.tsv 42 TRAITS both tsv stable - - file {sample}/traits/{sample}_traits.tsv 42 TRAITS both tsv stable - - file {sample}/traits/{sample}_traits_genotypes.tsv 42 TRAITS_SITES both tsv stable - - file {sample}/vcf/{sample}.g.vcf.gz 03 DEEPVARIANT both vcf stable - - file {sample}/vcf/{sample}.g.vcf.gz.tbi 03 DEEPVARIANT both index stable - - file {sample}/vcf/{sample}.report.html 07 - bash html stable bash - file {sample}/vcf/{sample}.report.json 07 - bash json stable bash - file {sample}/vcf/{sample}.vcf.gz 03 DEEPVARIANT both vcf stable bash FORMAT/GT,FORMAT/GQ,FORMAT/DP file {sample}/vcf/{sample}.vcf.gz.tbi 03 DEEPVARIANT both index stable bash - file {sample}/vcf/{sample}_roh.txt 11 - bash text stable bash - file {sample}/vcf/{sample}_roh_summary.txt 11 - bash tsv stable bash chrom,start,end,length_bp,length_mb file {sample}/vcf_gatk/{sample}.vcf.gz 03a - bash vcf stable bash FORMAT/GT file {sample}/vep/{sample}_annotated.vcf.gz 30 VCFANNO_INDEX both vcf stable both INFO/REVEL file {sample}/vep/{sample}_annotated.vcf.gz.tbi 30 VCFANNO_INDEX both index stable nextflow - file {sample}/vep/{sample}_vep.vcf.gz 13 VEP both vcf stable - - file {sample}/vep/{sample}_vep.vcf.gz.tbi 13 VEP both index stable - - file {sample}/vep/{sample}_vep.vcf_summary.html 13 VEP nextflow html stable - - file {sample}/viral/{sample}_human_coverage.tsv 47 VIRAL_READS both tsv experimental - - file {sample}/viral/{sample}_viral.tsv 47 VIRAL_REPORT both tsv experimental - - file {sample}/viral/{sample}_viral_coverage.tsv 47 VIRAL_READS both tsv experimental - - file {sample}/viral/{sample}_viral_depth.tsv 47 VIRAL_READS nextflow tsv internal - - file {sample}/viral/{sample}_viral_reads.bam 47 VIRAL_READS both bam experimental - - file {sample}/viral/{sample}_viral_reads.bam.bai 47 VIRAL_READS both index experimental - - file {sample}/vntyper/run 52 VNTYPER both dir experimental - - file {sample}/vntyper/{sample}_vntyper.log 52 VNTYPER both text experimental - - file {sample}/vntyper/{sample}_vntyper.tsv 52 VNTYPER both tsv experimental - - file {sample}/y_haplogroup/{sample}_chrY.bam 37 Y_PILEUP both bam experimental - - file {sample}/y_haplogroup/{sample}_chrY.bam.bai 37 Y_PILEUP both index experimental - - file {sample}/y_haplogroup/{sample}_idxstats.txt 37 Y_PILEUP nextflow text internal - - file {sample}/y_haplogroup/{sample}_y_haplogroup.txt 37 Y_HAPLOGROUP both text experimental - - file {sample}/y_haplogroup/{sample}_y_pileup.txt 37 Y_PILEUP nextflow text internal - - file {sample}/y_haplogroup/{sample}_y_private_snps.tsv 37 Y_PRIVATE both tsv experimental - - file {sample}/y_haplogroup/{sample}_y_tree.txt 37 Y_HAPLOGROUP both text experimental - - file {sample}/y_haplogroup/{sample}_y_tree_path.tsv 37 Y_HAPLOGROUP both tsv experimental - - file {sample}/y_haplogroup/{sample}_y_tree_pileup.txt 37 Y_PILEUP nextflow text internal - - file {sample}/y_str/{sample}_y_str.csv 45 Y_STR both csv experimental - - file {sample}/y_str/{sample}_y_str.log 45 Y_STR both text experimental - - file {sample}/y_str/{sample}_y_str.tsv 45 Y_STR both tsv experimental - - file {sample}/y_str/{sample}_y_str.vcf.gz 45 Y_STR both vcf experimental - - file {sample}/{sample}_charts.json 24 HTML_REPORT both json stable - - file {sample}/{sample}_report.html 24 HTML_REPORT both html stable bash - file {sample}/{sample}_report.txt 24 - both text stable bash - file {sample}/{sample}_search_index.json 24 HTML_REPORT both json stable - - file {sample}/{sample}_sex_check.tsv 16 INDEXCOV nextflow tsv stable - - param input - - - - stable - - param outdir - - - - stable - - param allow_unfiltered - - - - stable - - param publish_dir_mode - - - - stable - - param skip_trim - - - - stable - - param minimap2_index - - - - stable - - param intervals - - - - stable - - param sex_check - - - - stable - - param reference - - - - stable - - param clinvar - - - - stable - - param clinvar_index - - - - stable - - param tools - - - - stable - - param vep_cache - - - - stable - - param vep_cache_cpsr - - - - stable - - param pcgr_data - - - - stable - - param pypgx_bundle - - - - stable - - param cadd_snv - - - - stable - - param cadd_snv_index - - - - stable - - param cadd_indel - - - - stable - - param cadd_indel_index - - - - stable - - param spliceai_snv - - - - stable - - param spliceai_snv_index - - - - stable - - param spliceai_indel - - - - stable - - param spliceai_indel_index - - - - stable - - param revel - - - - stable - - param revel_index - - - - stable - - param alphamissense - - - - stable - - param alphamissense_index - - - - stable - - param gnomad_constraint - - - - stable - - param pgs_scoring - - - - stable - - param ancestry_ref - - - - stable - - param ancestry_fine_panel - - - - experimental - - param ancient_panel - - - - experimental - - param pgsc_calc - - - - stable - - param prs_keep_ambiguous - - - - stable - - param expansion_catalog - - - - stable - - param hla_dat - - - - stable - - param hla_genes - - - - stable - - param gencode_exons - - - - stable - - param mito_clinvar - - - - stable - - param gnomad_mito - - - - stable - - param kir - - - - experimental - - param kir_dat - - - - experimental - - param hla_qc - - - - experimental - - param cyrius_install - - - - stable - - param parascopy_data - - - - experimental - - param yleaf_data - - - - experimental - - param hpo - - - - experimental - - param exomiser_data - - - - experimental - - param pedigree - - - - experimental - - param family_name - - - - experimental - - param exomiser_proband - - - - experimental - - param exomiser_assembly - - - - experimental - - param medications - - - - experimental - - param archaic_data - - - - experimental - - param archaic_pop - - - - experimental - - param consumer_sites - - - - experimental - - param megane_kmers - - - - experimental - - param mocha_data - - - - experimental - - param locityper_data - - - - experimental - - param locityper_bg_region - - - - experimental - - param viral_ref - - - - experimental - - param chip_gff - - - - experimental - - param chip_germline_resource - - - - experimental - - param chip_pon - - - - experimental - - param parascopy_population - - - - experimental - - param parascopy_depth_bed - - - - experimental - - param paraphase_regions - - - - experimental - - param slivar_bin - - - - stable - - param cnvpytor_resources - - - - stable - - param annotsv_annotations - - - - stable - - param delly_exclude - - - - stable - - param manta_call_regions - - - - stable - - param cytoband - - - - stable - - param somalier_sites - - - - experimental - - param verifybamid2_panel - - - - experimental - - param freemix_warn - - - - experimental - - param max_cpus - - - - stable - - param max_memory - - - - stable - - param max_time - - - - stable - - tool pharmcat 07 - - - stable - - tool cpic 27 - - - stable - - tool clinvar 06 - - - stable - - tool pypgx 32 - - - stable - - tool vep 13 - - - stable - - tool vcfanno 30 - - - stable - - tool slivar 31 - - - stable - - tool clinical_filter 23 - - - stable - - tool cpsr 17 - - - stable - - tool roh 11 - - - stable - - tool prs 25 - - - stable - - tool ancestry 26 - - - stable - - tool ancestry_fine 26b - - - experimental - - tool mito_haplogroup 12 - - - stable - - tool hla_typing 08 - - - stable - - tool expansion_hunter 09 - - - stable - - tool stranger 09b - - - stable - - tool telomere_hunter 10 - - - stable - - tool mosdepth 16b - - - stable - - tool mito_variants 20 - - - stable - - tool cyrius 21 - - - stable - - tool manta 04 - - - stable - - tool delly 19 - - - stable - - tool cnvpytor 18 - - - stable - - tool duphold 15 - - - stable - - tool annotsv 05 - - - stable - - tool survivor_merge 22 - - - stable - - tool sample_qc 33 - - - experimental - - tool cram_archive 34 - - - experimental - - tool parascopy 35 - - - experimental - - tool paraphase 35b - - - experimental - - tool y_haplogroup 37 - - - experimental - - tool locityper 53 - - - experimental - - tool html_report 24 - - - stable - - tool multiqc 28 - - - stable - - tool consumer_export 40 - - - experimental - - tool bloodtype 41 - - - experimental - - tool lpa 46 - - - experimental - - tool vntyper 52 - - - experimental - - tool traits 42 - - - stable - - tool archaic 43 - - - experimental - - tool ancient 44 - - - experimental - - tool y_str 45 - - - experimental - - tool viral 47 - - - experimental - - tool exomiser 48 - - - experimental - - tool chip 49 - - - experimental - - tool mei 50 - - - experimental - - tool mocha 51 - - - experimental - - switch GENOME_DIR - - - - stable - - switch SKIP_VALIDATION - - - - stable - - switch THREADS - - - - stable - - switch SKIP_TRIM - - - - stable - - switch INTERVALS - - - - stable - - switch ALIGN_DIR - - - - stable - - switch TOOLS - - - - stable - - switch KIR - - - - experimental - - switch HLA_QC - - - - experimental - - switch HPO - - - - experimental - - switch REF_FASTA - - - - stable - - switch EH_CATALOG - - - - stable - - switch MANTA_CALL_REGIONS - - - - stable - - switch PARASCOPY_POPULATION - - - - experimental - - switch PARAPHASE_REGIONS - - - - experimental - - switch ANCESTRY_PANEL - - - - stable - - switch ANCESTRY_FINE_DIR - - - - experimental - - switch ARCHAIC_DIR - - - - experimental - - switch ARCHAIC_POP - - - - experimental - - switch PGSC_CALC_DIR - - - - stable - - switch ANCIENT_PANEL_DIR - - - - experimental - - switch VIRAL_REF - - - - experimental - - switch MEGANE_KMERS - - - - experimental - - switch MOCHA_DATA - - - - experimental - - switch GRIDSS - - - - stable - - switch IMPUTATION - - - - stable - - switch SOMATIC - - - - stable - - switch EXTRA_CALLERS - - - - stable - - switch BENCHMARK - - - - stable - - switch FAMILIES - - - - experimental - - switch OWNGENOME_LIVE_URL - - - - experimental - - switch LOCITYPER_DATA - - - - experimental - - switch LOCITYPER_BG_REGION - - - - experimental - - switch NXF_VER - - - - stable - - switch NXF_WORK - - - - stable - - switch NXF_HOME - - - - stable - - switch NXF_OFFLINE - - - - stable - -