Render diff - PR #1743

34 changed, 4 added out of 319 total renders. Generated 2026-08-15 08:32 UTC.

What is this page?

nf-metro generates metro-map-style SVG diagrams from Mermaid graph definitions. This page is automatically generated for every pull request and shows only the renders that changed compared to the main branch.

Use it to check that code changes produce the intended visual result without unexpected side-effects on other diagrams. Each entry shows the base (main) render on the left and the PR render on the right. Use the toggle buttons to switch between side-by-side, base-only, and PR-only views.

What to look for:

Layout-quality metrics

Advisory only — nothing gates on these. green improved, red regressed. Lower is better except in the ↑ column.

RenderCrossingsNear-horiz.Lone diag.Bends/routeCornersTurn/route (rad)Label strikesMarker gap ↑Excess gapsWasted canvas
aligner_row_terminator_lane_gap0000.5210.6→0.6 (−0.0)039.0061%
exit_run_three_drop_columns5000.3130.5060.1047%
leftward_up_exit_turn_order1000.7121.0060.0055%
multi_frame_exit_lane_settlement1000.3260.50110.8046%
target_lane_transition3000.5140.8088.0047%
bottom_exit_stacked_right_entry_fan0000.560.8070.0053%→53% (+0%)
funcprofiler_upstream35→27 (−8)01→0 (−1)1.2→1.0 (−0.2)98→86 (−12)1.5→1.4 (−0.1)039.0→46.4 (+7.4)1→8 (+7)55%→49% (−6%)
seed72_cross_family_fan0000.580.7070.1050%
bypass_fan_in_outer_slot4000.3220.4063.7→66.1 (+2.4)042%
bypass_leftward_far_side_entry0000.8281.2070.1→72.1 (+2.0)071%
bypass_leftward_overflow0000.8281.2070.1072%
convergent_offrow_exit_climb13001.2861.5028.0140%
disjoint_sameline_trunks6000.7161.0076.0066%
dogleg_exempt_distinct0000.9121.4060.1048%
bypass_left_entry_from_right0000.761.0078.0→76.0 (−2.0)050%→51% (+2%)
fold_stacked_branch2000.2160.3076.1→73.1 (−3.0)029%
packed_cell_right_exit_left_entry_wrap8001.3→1.2 (−0.1)861.5→1.5 (−0.1)043.4018%
reconverge_reversed_fold2000.2160.3076.1→73.1 (−3.0)029%
complex_multipath3000.3160.4073.0→74.6 (+1.6)051%
genomeassembly_organellar8000.9501.1039.0023%
seed_15–→51–→0–→0–→0.7–→73–→1.1–→0–→60.0–→0–→28%
seed_41–→93–→0–→0–→0.8–→119–→1.2–→0–→40.0–→0–→30%
seed_72–→14–→0–→0–→0.4–→28–→0.6–→0–→60.0–→0–→39%
seed_77–→62–→0–→0–→0.6–→92–→0.9–→0–→40.0–→0–→38%
target_entry_runway_bypass13000.81261.0060.0126%
junction_entry_reversed_fold0000.6100.9074.1061%
junction_fanout_convergence0000.781.0073.1068%
merge_bottom_row_bypass0000.580.8076.0038%
merge_feeder_shared_channel_gap0000.580.8076.0037%
merge_right_entry0000.6100.90–→n/a044%
legend_combo0000.4→0.2 (−0.2)4→2 (−2)0.3→0.2 (−0.2)036.0090%
longread_variant_calling15001.3951.7028.0121%
rowmate_tb_side_entry_top_align0000.91350.8→0.8 (−0.0)040.0220%
pipeline_variantbenchmarking3001.0961.2037.6715%
plan_owned_distinct_lane_separation6000.8201.3060.0065%
self_crossing_bridge0000.440.60–→n/a040%
variantbenchmarking3001.0961.2037.6715%
variantbenchmarking_auto4001.0961.2037.6515%

Changed renders

Multi-line Bundles

Fan-out and Fan-in

Bypass Routing

Serpentine Layout

Branching and Multipath

Test Fixtures

Merge & Convergence

Feature Showcase

Realistic Pipelines

nf-core Pipelines

Inter-section Routing

Basic Topologies

Guide Examples

Multi-line Bundles

Aligner Row Terminator Lane Gap changed

Base (main)

Aligner row vs pinned continuation 1 Pre-processing 2 Genome alignment & quantification 3 Post-processing STAR SAMtools Bowtie2 HISAT2 FastQC UMI-tools Dedup Picard RSEM Salmon tximport MultiQC Sum. Exp. preproc__exit_right_0 (right) genome_align__exit_right_1 (right) genome_align__entry_left_2 (left) postproc__entry_left_3 (left) col 0|1 col 1|2 row 0 grid row 0 grid _h1 _h2 _h3 STAR/RSEM STAR/Salmon Bowtie2/Salmon HISAT2 created with nf-metro v1.1.0+dev

PR

Aligner row vs pinned continuation 1 Pre-processing 2 Genome alignment & quantification 3 Post-processing STAR SAMtools Bowtie2 HISAT2 FastQC UMI-tools Dedup Picard RSEM Salmon tximport MultiQC Sum. Exp. preproc__exit_right_0 (right) genome_align__exit_right_1 (right) genome_align__entry_left_2 (left) postproc__entry_left_3 (left) col 0|1 col 1|2 row 0 grid row 0 grid _h1 _h2 _h3 STAR/RSEM STAR/Salmon Bowtie2/Salmon HISAT2 created with nf-metro v1.1.0+dev

Exit Run Three Drop Columns changed

Base (main)

Exit run, three drop columns 1 A 2 B 3 C 4 D 5 E Step A1 Step B1 Step C1 Step E1 Step D1 Step A2 Step B2 Step C2 Step E2 Step D2 Step B3 Step C3 Step B4 a__exit_right_0 (right) b__exit_right_1 (right) c__exit_right_2 (right) b__entry_left_3 (left) c__entry_left_4 (left) e__entry_left_5 (left) d__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __junction_9 (?) __merge_3 (?) __merge_4 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid Main Report Sheets created with nf-metro v1.1.0+dev

PR

Exit run, three drop columns 1 A 2 B 3 C 4 D 5 E Step A1 Step B1 Step C1 Step E1 Step D1 Step A2 Step B2 Step C2 Step E2 Step D2 Step B3 Step C3 Step B4 a__exit_right_0 (right) b__exit_right_1 (right) c__exit_right_2 (right) b__entry_left_3 (left) c__entry_left_4 (left) e__entry_left_5 (left) d__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __junction_9 (?) __merge_3 (?) __merge_4 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid Main Report Sheets created with nf-metro v1.1.0+dev

Leftward Up Exit Turn Order changed

Base (main)

Leftward Upward Exit Turns 1 Feeder A 2 Feeder B 5 Target 3 Source 4 Auxiliary Source A Feed A Feed B Target Auxiliary Source B Shared Split feeder_a__exit_right_0 (right) feeder_b__exit_right_1 (right) auxiliary__exit_left_2 (left) source__exit_left_3 (left) source__entry_right_4 (right) target__entry_right_5 (right) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid Feed A Feed B Shared Terminator Branch created with nf-metro v1.1.0+dev

PR

Leftward Upward Exit Turns 1 Feeder A 2 Feeder B 5 Target 3 Source 4 Auxiliary Source A Feed A Feed B Target Auxiliary Source B Shared Split feeder_a__exit_right_0 (right) feeder_b__exit_right_1 (right) auxiliary__exit_left_2 (left) source__exit_left_3 (left) source__entry_right_4 (right) target__entry_right_5 (right) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid Feed A Feed B Shared Terminator Branch created with nf-metro v1.1.0+dev

Multi Frame Exit Lane Settlement changed

Base (main)

Independent Exit Lane Frames 1 Feeder 2 Settling source 3 Side 4 Straight target 5 Lower target 12 Independent target 11 Independentsource 6 Direct feeder 7 Direct source 8 Vertical direct target 9 Vertical side exit 10 Side report 13 Vertical source 14 Vertical target Before Direct in Vertical A Vertical C Side in Feed Side Straight Lower Independent in Independent out Direct feed Direct out Side result Split Direct done Vertical B Vertical D Side out Vertical E feeder__exit_right_0 (right) source__exit_right_1 (right) independent_source__exit_right_2 (right) direct_feeder__exit_right_3 (right) direct_source__exit_right_4 (right) side_work__exit_left_5 (left) vertical_up__exit_bottom_6 (bottom) source__entry_left_7 (left) side__entry_left_8 (left) straight_target__entry_left_9 (left) lower_target__entry_left_10 (left) independent_target__entry_left_11 (left) direct_source__entry_left_12 (left) direct_target__entry_left_13 (left) side_report__entry_right_14 (right) vertical_down__entry_top_15 (top) __junction_16 (?) __junction_17 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 3|4 row 0 grid row 0 grid row 1 grid row 0 grid row 1 grid row 3 grid row 3 grid row 0 grid row 0 grid row 0 grid row 2 grid row 2 grid row 3 grid row 4 grid Lower branch Straight branch Terminates locally Wrap branch Alpha Beta Vertical L1 Vertical L2 Vertical L3 Vertical L4 Side A Side B created with nf-metro v1.1.0+dev

PR

Independent Exit Lane Frames 1 Feeder 2 Settling source 3 Side 4 Straight target 5 Lower target 12 Independent target 11 Independentsource 6 Direct feeder 7 Direct source 8 Vertical direct target 9 Vertical side exit 10 Side report 13 Vertical source 14 Vertical target Before Direct in Vertical A Vertical C Side in Feed Side Straight Lower Independent in Independent out Direct feed Direct out Side result Split Direct done Vertical B Vertical D Side out Vertical E feeder__exit_right_0 (right) source__exit_right_1 (right) independent_source__exit_right_2 (right) direct_feeder__exit_right_3 (right) direct_source__exit_right_4 (right) side_work__exit_left_5 (left) vertical_up__exit_bottom_6 (bottom) source__entry_left_7 (left) side__entry_left_8 (left) straight_target__entry_left_9 (left) lower_target__entry_left_10 (left) independent_target__entry_left_11 (left) direct_source__entry_left_12 (left) direct_target__entry_left_13 (left) side_report__entry_right_14 (right) vertical_down__entry_top_15 (top) __junction_16 (?) __junction_17 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 3|4 row 0 grid row 0 grid row 1 grid row 0 grid row 1 grid row 3 grid row 3 grid row 0 grid row 0 grid row 0 grid row 2 grid row 2 grid row 3 grid row 4 grid Lower branch Straight branch Terminates locally Wrap branch Alpha Beta Vertical L1 Vertical L2 Vertical L3 Vertical L4 Side A Side B created with nf-metro v1.1.0+dev

Target Lane Transition changed

Base (main)

Target-side lane transition 1 Upstream 2 Branch 3 Source 4 Straight target 5 Lower target Enter Feed Branch end Straight Lower Leave upstream__exit_right_0 (right) source__exit_right_1 (right) source__entry_left_2 (left) upstream_branch__entry_left_3 (left) straight_target__entry_left_4 (left) lower_target__entry_left_5 (left) __junction_6 (?) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 1 grid row 2 grid row 0 grid row 0 grid row 1 grid First branch Second branch Local stage Third branch created with nf-metro v1.1.0+dev

PR

Target-side lane transition 1 Upstream 2 Branch 3 Source 4 Straight target 5 Lower target Enter Feed Branch end Straight Lower Leave upstream__exit_right_0 (right) source__exit_right_1 (right) source__entry_left_2 (left) upstream_branch__entry_left_3 (left) straight_target__entry_left_4 (left) lower_target__entry_left_5 (left) __junction_6 (?) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 1 grid row 2 grid row 0 grid row 0 grid row 1 grid First branch Second branch Local stage Third branch created with nf-metro v1.1.0+dev

Fan-out and Fan-in

Bottom Exit Stacked Right Entry Fan changed

Base (main)

Bottom-exit Fan to Stacked Right Entries 1 Vertical source 2 Upper target 3 Lower target Prepare Upper in Lower in Split Upper done Lower done source__exit_bottom_0 (bottom) upper_target__entry_right_1 (right) lower_target__entry_right_2 (right) __junction_3 (?) row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid Upper branch Lower branch created with nf-metro v1.1.0+dev

PR

Bottom-exit Fan to Stacked Right Entries 1 Vertical source 2 Upper target 3 Lower target Prepare Upper in Lower in Split Upper done Lower done source__exit_bottom_0 (bottom) upper_target__entry_right_1 (right) lower_target__entry_right_2 (right) __junction_3 (?) row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid Upper branch Lower branch created with nf-metro v1.1.0+dev

Funcprofiler Upstream changed

Base (main)

nf-core/funcprofiler (upstream) 1 Input 2 Functional Profiling 3 Quality Check 4 Output Short Reads Input Databases HUMAnN v3 MultiQC Results Directory HUMAnN v4 FMH FunProfiler RGI mifaser DIAMOND eggNOG-mapper Preprocess MERGE_RUNS input__exit_right_0 (right) profiling__exit_right_1 (right) QC__exit_right_2 (right) profiling__entry_left_3 (left) QC__entry_left_4 (left) Output__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) col 0|1 col 1|2 col 2|3 row 0 grid Preprocessing & QC Merge & Concat Database Prep HUMAnN v3 HUMAnN v4 FMH FunProfiler RGI mifaser DIAMOND eggNOG-mapper Reporting created with nf-metro v1.1.0+dev

PR

nf-core/funcprofiler (upstream) 1 Input 2 Functional Profiling 3 Quality Check 4 Output Short Reads Input Databases HUMAnN v3 MultiQC Results Directory HUMAnN v4 FMH FunProfiler RGI mifaser DIAMOND eggNOG-mapper Preprocess MERGE_RUNS input__exit_right_0 (right) profiling__exit_right_1 (right) QC__exit_right_2 (right) profiling__entry_left_3 (left) QC__entry_left_4 (left) Output__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) col 0|1 col 1|2 col 2|3 row 0 grid __bypass_merge_sr_qc_1 Preprocessing & QC Merge & Concat Database Prep HUMAnN v3 HUMAnN v4 FMH FunProfiler RGI mifaser DIAMOND eggNOG-mapper Reporting created with nf-metro v1.1.0+dev

Seed72 Cross Family Fan changed

Base (main)

Cross-family Fan from Frozen Seed 72 1 Source 2 Intervening work 4 Normal target 3 Reverse-flowtarget Prepare Blocked in Exempt in Normal in Split Blocked out Exempt done source__exit_right_0 (right) blocker__entry_left_1 (left) normal_target__entry_left_2 (left) exempt_target__entry_right_3 (right) __junction_4 (?) col 0|1 col 1|2 row 0|2 row 0 grid row 0 grid row 0 grid row 2 grid Through blocker Normal dogleg Exempt continuation created with nf-metro v1.1.0+dev

PR

Cross-family Fan from Frozen Seed 72 1 Source 2 Intervening work 4 Normal target 3 Reverse-flowtarget Prepare Blocked in Exempt in Normal in Split Blocked out Exempt done source__exit_right_0 (right) blocker__entry_left_1 (left) normal_target__entry_left_2 (left) exempt_target__entry_right_3 (right) __junction_4 (?) col 0|1 col 1|2 row 0|2 row 0 grid row 0 grid row 0 grid row 2 grid Through blocker Normal dogleg Exempt continuation created with nf-metro v1.1.0+dev

Bypass Routing

Bypass Fan In Outer Slot changed

Base (main)

Bypass Fan-in Outer Slot 1 Ingest 2 Trim & QC 3 Branch Hub 4 Alignment 5 Quantification 6 Peak Calling 7 Integration Samplesheet Fastp BWA-MEM MOFA Factor Model Salmon MACS2 Dispatch Demultiplex Contam Screen MarkDup MultiQC Report Tximport Annotate Peaks ingest__exit_right_0 (right) trim__exit_right_1 (right) hub__exit_right_2 (right) align_right__exit_right_3 (right) quant_bottom__exit_right_4 (right) peaks_bottom__exit_right_5 (right) trim__entry_left_6 (left) hub__entry_left_7 (left) align_right__entry_left_8 (left) quant_bottom__entry_left_9 (left) peaks_bottom__entry_left_10 (left) integrate__entry_left_11 (left) __junction_12 (?) __junction_13 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid DNA Methylation RNA ATAC QC created with nf-metro v1.1.0+dev

PR

Bypass Fan-in Outer Slot 1 Ingest 2 Trim & QC 3 Branch Hub 4 Alignment 5 Quantification 6 Peak Calling 7 Integration Samplesheet Fastp BWA-MEM MOFA Factor Model Salmon MACS2 Dispatch Demultiplex Contam Screen MarkDup MultiQC Report Tximport Annotate Peaks ingest__exit_right_0 (right) trim__exit_right_1 (right) hub__exit_right_2 (right) align_right__exit_right_3 (right) quant_bottom__exit_right_4 (right) peaks_bottom__exit_right_5 (right) trim__entry_left_6 (left) hub__entry_left_7 (left) align_right__entry_left_8 (left) quant_bottom__entry_left_9 (left) peaks_bottom__entry_left_10 (left) integrate__entry_left_11 (left) __junction_12 (?) __junction_13 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid DNA Methylation RNA ATAC QC created with nf-metro v1.1.0+dev

Bypass Leftward Far Side Entry changed

Base (main)

Seven-line leftward bypass far-side entry 1 Source 3 Middle 2 Target Start Mid Process Out MidOut End src_sec__exit_left_0 (left) tgt_sec__entry_left_1 (left) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid L1 L2 L3 L4 L5 L6 L7 created with nf-metro v1.1.0+dev

PR

Seven-line leftward bypass far-side entry 1 Source 3 Middle 2 Target Start Mid Process Out MidOut End src_sec__exit_left_0 (left) tgt_sec__entry_left_1 (left) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid L1 L2 L3 L4 L5 L6 L7 created with nf-metro v1.1.0+dev

Bypass Leftward Overflow changed

Base (main)

Seven-line reverse-flow bypass overflow 1 Source 3 Middle 2 Target Start Mid Process Out MidOut End src_sec__exit_left_0 (left) tgt_sec__entry_right_1 (right) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid L1 L2 L3 L4 L5 L6 L7 created with nf-metro v1.1.0+dev

PR

Seven-line reverse-flow bypass overflow 1 Source 3 Middle 2 Target Start Mid Process Out MidOut End src_sec__exit_left_0 (left) tgt_sec__entry_right_1 (right) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid L1 L2 L3 L4 L5 L6 L7 created with nf-metro v1.1.0+dev

Convergent Offrow Exit Climb changed

Base (main)

Long-read Variant Calling 1 Pre-processing 2 Small variant calling 5 CNVs 3 Repeats 4 Phasing 6 Structural Variants 7 Joint Calling 8 Annotation 9 Reports FASTQ BAM uBAM Sniffles WhatsHap Phase CuteSV Clair3 ont-spectre CNVCaller LongTR Jasmine merge samples VEP Geneyx Deepvariant Straglr GLNexus SnpEff SV Report TRGT AnnotSV samtoolsmerge cat FASTQ WhatsHap Haplotag Jasmine merge callers minimap2 samtoolssort/index mosdepth preprocessing__exit_right_0 (right) tr_calling__exit_right_1 (right) small_variants__exit_right_2 (right) phasing__exit_right_3 (right) cnv_calling__exit_right_4 (right) structural_variants__exit_right_5 (right) annotation__exit_right_6 (right) jointcalling__exit_right_7 (right) small_variants__entry_left_8 (left) tr_calling__entry_left_9 (left) cnv_calling__entry_left_10 (left) reports__entry_left_11 (left) phasing__entry_left_12 (left) jointcalling__entry_left_13 (left) annotation__entry_left_14 (left) structural_variants__entry_left_15 (left) __junction_16 (?) __junction_17 (?) __junction_18 (?) __junction_19 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 row 0|1 row 0 grid row 1 grid uBAM FASTQ BAM Other SNV VCF SV VCF created with nf-metro v1.1.0+dev

PR

Long-read Variant Calling 1 Pre-processing 2 Small variant calling 5 CNVs 3 Repeats 4 Phasing 6 Structural Variants 7 Joint Calling 8 Annotation 9 Reports FASTQ BAM uBAM Sniffles WhatsHap Phase CuteSV Clair3 ont-spectre CNVCaller LongTR Jasmine merge samples VEP Geneyx Deepvariant Straglr GLNexus SnpEff SV Report TRGT AnnotSV samtoolsmerge cat FASTQ WhatsHap Haplotag Jasmine merge callers minimap2 samtoolssort/index mosdepth preprocessing__exit_right_0 (right) tr_calling__exit_right_1 (right) small_variants__exit_right_2 (right) phasing__exit_right_3 (right) cnv_calling__exit_right_4 (right) structural_variants__exit_right_5 (right) annotation__exit_right_6 (right) jointcalling__exit_right_7 (right) small_variants__entry_left_8 (left) tr_calling__entry_left_9 (left) cnv_calling__entry_left_10 (left) reports__entry_left_11 (left) phasing__entry_left_12 (left) jointcalling__entry_left_13 (left) annotation__entry_left_14 (left) structural_variants__entry_left_15 (left) __junction_16 (?) __junction_17 (?) __junction_18 (?) __junction_19 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 row 0|1 row 0 grid row 1 grid uBAM FASTQ BAM Other SNV VCF SV VCF created with nf-metro v1.1.0+dev

Disjoint Sameline Trunks changed

Base (main)

Disjoint Same-Line Bypass Trunks 1 Ingest 2 QC 3 Align 4 Call 5 Report Input QC Step Align Call Report secA__exit_right_0 (right) secB__exit_right_1 (right) secC__exit_right_2 (right) secD__exit_right_3 (right) secB__entry_left_4 (left) secC__entry_left_5 (left) secD__entry_left_6 (left) secE__entry_left_7 (left) __junction_8 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid Line A Line B Line C created with nf-metro v1.1.0+dev

PR

Disjoint Same-Line Bypass Trunks 1 Ingest 2 QC 3 Align 4 Call 5 Report Input QC Step Align Call Report secA__exit_right_0 (right) secB__exit_right_1 (right) secC__exit_right_2 (right) secD__exit_right_3 (right) secB__entry_left_4 (left) secC__entry_left_5 (left) secD__entry_left_6 (left) secE__entry_left_7 (left) __junction_8 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid Line A Line B Line C created with nf-metro v1.1.0+dev

Dogleg Exempt Distinct changed

Base (main)

Dogleg Off Exempt Trunks - Distinct Line Regime 3 Left Target 2 Right Source 4 Bottom Sink 1 Skip Source Collect Input R Collect B Step S Output Hub R Output B Out S right_src__exit_right_0 (right) left_tgt__exit_right_1 (right) skip_src__exit_right_2 (right) left_tgt__entry_left_3 (left) bot_sink__entry_left_4 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 1 grid row 1 grid Wrap Bypass Skip created with nf-metro v1.1.0+dev

PR

Dogleg Off Exempt Trunks - Distinct Line Regime 3 Left Target 2 Right Source 4 Bottom Sink 1 Skip Source Collect Input R Collect B Step S Output Hub R Output B Out S right_src__exit_right_0 (right) left_tgt__exit_right_1 (right) skip_src__exit_right_2 (right) left_tgt__entry_left_3 (left) bot_sink__entry_left_4 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 1 grid row 1 grid Wrap Bypass Skip created with nf-metro v1.1.0+dev

Serpentine Layout

Bypass Left Entry From Right changed

Base (main)

Bypass into a far LEFT entry from a junction 2 Target 4 Intervening section 1 Source 3 Sibling Blocker start Target step Source step Sibling step Blocker end source__exit_left_0 (left) target__entry_left_1 (left) sibling__entry_left_2 (left) __junction_3 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 1 grid Main Side Obstacle created with nf-metro v1.1.0+dev

PR

Bypass into a far LEFT entry from a junction 2 Target 4 Intervening section 1 Source 3 Sibling Blocker start Target step Source step Sibling step Blocker end source__exit_left_0 (left) target__entry_left_1 (left) sibling__entry_left_2 (left) __junction_3 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 1 grid Main Side Obstacle created with nf-metro v1.1.0+dev

Fold Stacked Branch changed

Base (main)

Single-Cell Multi-Omics Pipeline 1 Preprocessing 2 RNA Analysis 3 ATAC Analysis 4 Protein Analysis 5 Multi-Modal Integration 6 Biological Interpretation 7 Technical QC 8 Final Report Input Normalize Merge Modalities Cell Typing Aggregate Peak Calling Normalize Doublet Detection Demux Cluster WNN Trajectory Render Report Motif Analysis Quantify Ambient RNA Raw QC Markers UMAP Gene Reg. Network Footprinting Visualize QC Metrics Trim Trajectories Coverage Filter DGE Clean QC Classify Sort preprocessing__exit_right_0 (right) rna_analysis__exit_right_1 (right) atac_analysis__exit_right_2 (right) protein_analysis__exit_right_3 (right) integration__exit_bottom_4 (bottom) bio_interp__exit_left_5 (left) tech_qc__exit_left_6 (left) rna_analysis__entry_left_7 (left) atac_analysis__entry_left_8 (left) protein_analysis__entry_left_9 (left) integration__entry_left_10 (left) bio_interp__entry_right_11 (right) tech_qc__entry_right_12 (right) final_report__entry_right_13 (right) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 3|4 row 0 grid row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 4 grid row 3 grid scRNA-seq scATAC-seq CITE-seq created with nf-metro v1.1.0+dev

PR

Single-Cell Multi-Omics Pipeline 1 Preprocessing 2 RNA Analysis 3 ATAC Analysis 4 Protein Analysis 5 Multi-Modal Integration 6 Biological Interpretation 7 Technical QC 8 Final Report Input Normalize Merge Modalities Cell Typing Aggregate Peak Calling Normalize Doublet Detection Demux Cluster WNN Trajectory Render Report Motif Analysis Quantify Ambient RNA Raw QC Markers UMAP Gene Reg. Network Footprinting Visualize QC Metrics Trim Trajectories Coverage Filter DGE Clean QC Classify Sort preprocessing__exit_right_0 (right) rna_analysis__exit_right_1 (right) atac_analysis__exit_right_2 (right) protein_analysis__exit_right_3 (right) integration__exit_bottom_4 (bottom) bio_interp__exit_left_5 (left) tech_qc__exit_left_6 (left) rna_analysis__entry_left_7 (left) atac_analysis__entry_left_8 (left) protein_analysis__entry_left_9 (left) integration__entry_left_10 (left) bio_interp__entry_right_11 (right) tech_qc__entry_right_12 (right) final_report__entry_right_13 (right) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 3|4 row 0 grid row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 4 grid row 3 grid scRNA-seq scATAC-seq CITE-seq created with nf-metro v1.1.0+dev

Packed Cell Right Exit Left Entry Wrap changed

Base (main)

nf-core/genomeassembler 1 Inputs 2 Prepare 3 Assemble 4 Polish 5 Scaffold 6 QC 7 Annotation FASTA assembly FASTA assembly FASTA polished assembly FASTA (polished) assembly FASTA scaffolded assembly FASTA fasta FASTA assembly short reads ONT reads HiFi reads hifiasmflye Reference genome Reference annotation hifiasm_ul HiC reads Scaffold:ONT / HiFi fastplong fastp pilon k-mer: meryl / merqury medakadorado Ref:RagTag longstitchLINKS liftoff QUAST HiC:yahs BUSCO input__exit_right_0 (right) prep__exit_right_1 (right) assemble__exit_right_2 (right) polish__exit_right_3 (right) prep__entry_left_4 (left) assemble__entry_left_5 (left) qc__entry_left_6 (left) polish__entry_left_7 (left) scaffold__entry_left_8 (left) annot__entry_left_9 (left) __junction_10 (?) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _input_out __converge_assembly_file_out_1 __converge_polished_file_2 __converge_scaffolded_out_3 short genomic ONT HiFi refs assembly HiC annotation QC created with nf-metro v1.1.0+dev

PR

nf-core/genomeassembler 1 Inputs 2 Prepare 3 Assemble 4 Polish 5 Scaffold 6 QC 7 Annotation FASTA assembly FASTA assembly FASTA polished assembly FASTA (polished) assembly FASTA scaffolded assembly FASTA fasta FASTA assembly short reads ONT reads HiFi reads hifiasmflye Reference genome Reference annotation hifiasm_ul HiC reads Scaffold:ONT / HiFi fastplong fastp pilon k-mer: meryl / merqury medakadorado Ref:RagTag longstitchLINKS liftoff QUAST HiC:yahs BUSCO input__exit_right_0 (right) prep__exit_right_1 (right) assemble__exit_right_2 (right) polish__exit_right_3 (right) prep__entry_left_4 (left) assemble__entry_left_5 (left) qc__entry_left_6 (left) polish__entry_left_7 (left) scaffold__entry_left_8 (left) annot__entry_left_9 (left) __junction_10 (?) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _input_out __converge_assembly_file_out_1 __converge_polished_file_2 __converge_scaffolded_out_3 short genomic ONT HiFi refs assembly HiC annotation QC created with nf-metro v1.1.0+dev

Reconverge Reversed Fold changed

Base (main)

Reconvergence Reversed Alt 1 Preprocessing 2 RNA Analysis 3 ATAC Analysis 4 Protein Analysis 5 Multi-Modal Integration 6 Biological Interpretation 7 Technical QC 8 Final Report Input Normalize Merge Modalities Cell Typing Aggregate Normalize Doublet Detection Peak Calling Demux Cluster WNN Trajectory Render Report Quantify Ambient RNA Motif Analysis Raw QC Markers UMAP Gene Reg. Network Visualize QC Metrics Footprinting Trim Trajectories Coverage Filter DGE Clean QC Classify Sort preprocessing__exit_right_0 (right) rna_analysis__exit_right_1 (right) atac_analysis__exit_right_2 (right) protein_analysis__exit_right_3 (right) integration__exit_bottom_4 (bottom) bio_interp__exit_left_5 (left) tech_qc__exit_left_6 (left) rna_analysis__entry_left_7 (left) atac_analysis__entry_left_8 (left) protein_analysis__entry_left_9 (left) integration__entry_left_10 (left) bio_interp__entry_right_11 (right) tech_qc__entry_right_12 (right) final_report__entry_right_13 (right) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 3|4 row 0 grid row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 4 grid row 3 grid scRNA-seq CITE-seq scATAC-seq created with nf-metro v1.1.0+dev

PR

Reconvergence Reversed Alt 1 Preprocessing 2 RNA Analysis 3 ATAC Analysis 4 Protein Analysis 5 Multi-Modal Integration 6 Biological Interpretation 7 Technical QC 8 Final Report Input Normalize Merge Modalities Cell Typing Aggregate Normalize Doublet Detection Peak Calling Demux Cluster WNN Trajectory Render Report Quantify Ambient RNA Motif Analysis Raw QC Markers UMAP Gene Reg. Network Visualize QC Metrics Footprinting Trim Trajectories Coverage Filter DGE Clean QC Classify Sort preprocessing__exit_right_0 (right) rna_analysis__exit_right_1 (right) atac_analysis__exit_right_2 (right) protein_analysis__exit_right_3 (right) integration__exit_bottom_4 (bottom) bio_interp__exit_left_5 (left) tech_qc__exit_left_6 (left) rna_analysis__entry_left_7 (left) atac_analysis__entry_left_8 (left) protein_analysis__entry_left_9 (left) integration__entry_left_10 (left) bio_interp__entry_right_11 (right) tech_qc__entry_right_12 (right) final_report__entry_right_13 (right) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 3|4 row 0 grid row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 4 grid row 3 grid scRNA-seq CITE-seq scATAC-seq created with nf-metro v1.1.0+dev

Branching and Multipath

Complex Multipath changed

Base (main)

Complex Multipath 1 Input 2 Fast Track 3 Full Pre-process 5 Standard Analysis 4 Deep Analysis 6 Output Raw Data Quick Align Aggregate Trim Align HQ Align Validate Quick Quant Report Filter Quantify Dedup QC Check HQ Quantify input_sec__exit_right_0 (right) full_preprocess__exit_right_1 (right) fast_track__exit_right_2 (right) standard_analysis__exit_right_3 (right) deep_analysis__exit_right_4 (right) fast_track__entry_left_5 (left) full_preprocess__entry_left_6 (left) standard_analysis__entry_left_7 (left) deep_analysis__entry_left_8 (left) output_sec__entry_left_9 (left) __junction_10 (?) __junction_11 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 0 grid row 1 grid row 0 grid row 1 grid row 0 grid Fast Path Standard Path Detailed Analysis Legacy Path created with nf-metro v1.1.0+dev

PR

Complex Multipath 1 Input 2 Fast Track 3 Full Pre-process 5 Standard Analysis 4 Deep Analysis 6 Output Raw Data Quick Align Aggregate Trim Align HQ Align Validate Quick Quant Report Filter Quantify Dedup QC Check HQ Quantify input_sec__exit_right_0 (right) full_preprocess__exit_right_1 (right) fast_track__exit_right_2 (right) standard_analysis__exit_right_3 (right) deep_analysis__exit_right_4 (right) fast_track__entry_left_5 (left) full_preprocess__entry_left_6 (left) standard_analysis__entry_left_7 (left) deep_analysis__entry_left_8 (left) output_sec__entry_left_9 (left) __junction_10 (?) __junction_11 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 0 grid row 1 grid row 0 grid row 1 grid row 0 grid Fast Path Standard Path Detailed Analysis Legacy Path created with nf-metro v1.1.0+dev

Test Fixtures

Genomeassembly Organellar changed

Base (main)

sanger-tol/genomeassembly 1 Raw assembly 2 Purging 4 Polishing 5 Scaffolding 6 Genome QC 3 Organellar assembly FASTX CRAM FASTQ FASTX bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO MitoHiFi hifiasm oatk MerquryFK PretextMap FreeBayes Juicer Cooler raw_asm__exit_right_0 (right) purging__exit_right_1 (right) polishing__exit_right_2 (right) scaffolding__exit_right_3 (right) purging__entry_left_4 (left) scaffolding__entry_left_5 (left) polishing__entry_left_6 (left) genome_statistics__entry_left_7 (left) organellar_assembly__entry_left_8 (left) __junction_9 (?) __junction_10 (?) __junction_11 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid row 4 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

PR

sanger-tol/genomeassembly 1 Raw assembly 2 Purging 4 Polishing 5 Scaffolding 6 Genome QC 3 Organellar assembly FASTX CRAM FASTQ FASTX bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO MitoHiFi hifiasm oatk MerquryFK PretextMap FreeBayes Juicer Cooler raw_asm__exit_right_0 (right) purging__exit_right_1 (right) polishing__exit_right_2 (right) scaffolding__exit_right_3 (right) purging__entry_left_4 (left) scaffolding__entry_left_5 (left) polishing__entry_left_6 (left) genome_statistics__entry_left_7 (left) organellar_assembly__entry_left_8 (left) __junction_9 (?) __junction_10 (?) __junction_11 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid row 4 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

Seed 15 added

New in PR

Candidate recovery fuzz 1 Section0 2 Section 1 3 Section 2 5 Section3 4 Section4 6 Section 5 7 Section 6 8 Section 7 9 Section8 10 Section 9 11 Section 10 N2.0 N5.0 N6.0 N1.0 N7.0 N9.0 N10.0 N0.0 N3.0 N4.0 N8.0 N2.1 N5.1 N6.1 N1.1 N7.1 N9.1 N10.1 N6.2 N9.2 N10.2 N10.3 s0__exit_right_0 (right) s1__exit_right_1 (right) s2__exit_right_2 (right) s3__exit_left_3 (left) s4__exit_left_4 (left) s5__exit_left_5 (left) s6__exit_left_6 (left) s7__exit_left_7 (left) s8__exit_left_8 (left) s9__exit_left_9 (left) s1__entry_left_10 (left) s4__entry_right_11 (right) s2__entry_left_12 (left) s3__entry_left_13 (left) s6__entry_right_14 (right) s9__entry_right_15 (right) s5__entry_right_16 (right) s8__entry_right_17 (right) s7__entry_right_18 (right) s10__entry_right_19 (right) __junction_20 (?) __junction_21 (?) __junction_22 (?) __junction_23 (?) __junction_24 (?) __junction_25 (?) __junction_26 (?) __junction_27 (?) __merge_8 (?) __merge_9 (?) __merge_10 (?) __merge_11 (?) __merge_12 (?) __merge_13 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 row 0|1 row 1|2 row 0 grid row 0 grid row 0 grid row 1 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid Line 1 Line 2 Line 3 created with nf-metro v1.1.0+dev

Seed 41 added

New in PR

Candidate recovery fuzz 1 Section 0 2 Section 1 3 Section 2 5 Section 3 6 Section 4 4 Section5 8 Section6 10 Section 7 11 Section8 7 Section 9 9 Section 10 12 Section 11 13 Section 12 14 Section 13 N0.0 N1.0 N3.0 N5.0 N9.0 N4.0 N12.0 N13.0 N2.0 N7.0 N10.0 N11.0 N6.0 N8.0 N0.1 N1.1 N3.1 N5.1 N9.1 N4.1 N12.1 N13.1 N2.1 N7.1 N10.1 N11.1 N3.2 N5.2 N9.2 N4.2 N12.2 N2.2 N5.3 N9.3 N2.3 s0__exit_right_0 (right) s1__exit_right_1 (right) s2__exit_right_2 (right) s3__exit_right_3 (right) s4__exit_left_4 (left) s5__exit_left_5 (left) s6__exit_left_6 (left) s7__exit_left_7 (left) s8__exit_left_8 (left) s9__exit_left_9 (left) s10__exit_left_10 (left) s11__exit_left_11 (left) s1__entry_left_12 (left) s2__entry_left_13 (left) s5__entry_left_14 (left) s12__entry_right_15 (right) s3__entry_left_16 (left) s4__entry_right_17 (right) s9__entry_right_18 (right) s10__entry_right_19 (right) s13__entry_right_20 (right) s6__entry_right_21 (right) s7__entry_right_22 (right) s8__entry_right_23 (right) s11__entry_right_24 (right) __junction_25 (?) __junction_26 (?) __junction_27 (?) __junction_28 (?) __junction_29 (?) __junction_30 (?) __junction_31 (?) __junction_32 (?) __junction_33 (?) __merge_9 (?) __merge_10 (?) __merge_11 (?) __merge_12 (?) __merge_13 (?) __merge_14 (?) __merge_15 (?) __merge_16 (?) __merge_17 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 col 6|7 col 7|8 row 0|1 row 1|2 row 0 grid row 0 grid row 1 grid row 0 grid row 2 grid row 1 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid row 2 grid Line 1 Line 2 Line 3 Line 4 Line 5 created with nf-metro v1.1.0+dev

Seed 72 added

New in PR

Candidate recovery fuzz 1 Section 0 2 Section 1 4 Section 2 9 Section 3 3 Section 4 5 Section 5 6 Section 6 7 Section 7 8 Section 8 N3.0 N7.0 N8.0 N0.0 N2.0 N5.0 N1.0 N6.0 N4.0 N3.1 N7.1 N8.1 N0.1 N2.1 N5.1 N1.1 N6.1 N4.1 N3.2 N7.2 N2.2 N5.2 N1.2 N7.3 s0__exit_right_0 (right) s2__exit_right_1 (right) s3__exit_right_2 (right) s5__exit_right_3 (right) s6__exit_left_4 (left) s7__exit_left_5 (left) s1__entry_left_6 (left) s2__entry_left_7 (left) s3__entry_left_8 (left) s4__entry_left_9 (left) s7__entry_right_10 (right) s5__entry_left_11 (left) s6__entry_right_12 (right) s8__entry_right_13 (right) __junction_14 (?) __junction_15 (?) __junction_16 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 0 grid row 0 grid row 1 grid row 2 grid row 0 grid row 1 grid row 3 grid row 3 grid row 3 grid Line 1 Line 2 Line 3 Line 4 Line 5 Line 6 Line 7 created with nf-metro v1.1.0+dev

Seed 77 added

New in PR

Candidate recovery fuzz 1 Section 0 2 Section 1 3 Section 2 8 Section 3 9 Section4 10 Section 5 4 Section 6 11 Section 7 12 Section 8 13 Section9 14 Section 10 5 Section 11 15 Section 12 16 Section 13 6 Section 14 7 Section 15 17 Section 16 18 Section 17 19 Section 18 20 Section19 N1.0 N5.0 N3.0 N10.0 N6.0 N12.0 N14.0 N15.0 N16.0 N2.0 N8.0 N17.0 N18.0 N0.0 N7.0 N13.0 N4.0 N9.0 N11.0 N19.0 N1.1 N5.1 N3.1 N10.1 N6.1 N12.1 N14.1 N15.1 N16.1 N2.1 N8.1 N17.1 N18.1 N0.1 N7.1 N13.1 N5.2 N10.2 N6.2 N12.2 N15.2 N17.2 N18.2 N0.2 N6.3 N12.3 N15.3 s0__exit_right_0 (right) s1__exit_right_1 (right) s2__exit_right_2 (right) s3__exit_left_3 (left) s4__exit_left_4 (left) s5__exit_left_5 (left) s6__exit_right_6 (right) s7__exit_left_7 (left) s10__exit_left_8 (left) s11__exit_right_9 (right) s12__exit_left_10 (left) s13__exit_left_11 (left) s14__exit_right_12 (right) s15__exit_left_13 (left) s17__exit_left_14 (left) s18__exit_left_15 (left) s1__entry_left_16 (left) s5__entry_right_17 (right) s16__entry_right_18 (right) s2__entry_left_19 (left) s3__entry_right_20 (right) s4__entry_right_21 (right) s6__entry_left_22 (left) s8__entry_right_23 (right) s19__entry_right_24 (right) s9__entry_right_25 (right) s17__entry_right_26 (right) s7__entry_right_27 (right) s11__entry_left_28 (left) s10__entry_right_29 (right) s18__entry_right_30 (right) s12__entry_right_31 (right) s14__entry_left_32 (left) s13__entry_right_33 (right) s15__entry_left_34 (left) __junction_35 (?) __junction_36 (?) __junction_37 (?) __junction_38 (?) __junction_39 (?) __junction_40 (?) __junction_41 (?) __junction_42 (?) __junction_43 (?) __junction_44 (?) __junction_45 (?) __merge_11 (?) __merge_12 (?) __merge_13 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 col 6|7 col 7|8 col 8|9 col 9|10 col 10|11 col 11|12 row 0|1 row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid row 0 grid row 1 grid row 1 grid row 1 grid row 1 grid row 0 grid row 1 grid row 1 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid row 1 grid Line 1 Line 2 Line 3 Line 4 Line 5 created with nf-metro v1.1.0+dev

Target Entry Runway Bypass changed

Base (main)

1 Pre-processing 2 Alignment 3 Branch A 4 Branch B 5 Feeder L1 6 Feeder L2 8 Target 7 Reporting OUT OUT OUT OUT OUT OUT OUT BB0 BB2 AL0 BB4 FL1 FM2 Station C RP0 BA0 BB5 FL0 FM0 Station A BB6 BB1 T2 T3 PP1 AL1 FL2 T4 BA1 FM1 Station B BB3 PP2 FL3 BA2 T0 T1 PP3 BB7 PP4 PP5 PP6 PP7 PP8 PP9 PP10 PP11 PP12 branch_b__exit_left_0 (left) prep__exit_right_1 (right) align__exit_right_2 (right) branch_a__exit_right_3 (right) feeder_l1__exit_left_4 (left) feeder_l2__exit_right_5 (right) feeder_l1__entry_right_6 (right) align__entry_left_7 (left) branch_a__entry_left_8 (left) branch_b__entry_right_9 (right) feeder_l2__entry_left_10 (left) target__entry_left_11 (left) report__entry_left_12 (left) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 2 grid row 1 grid row 2 grid __converge_ff2_1 Line 1 Line 2 Line 3 created with nf-metro v1.1.0+dev

PR

1 Pre-processing 2 Alignment 3 Branch A 4 Branch B 5 Feeder L1 6 Feeder L2 8 Target 7 Reporting OUT OUT OUT OUT OUT OUT OUT BB0 BB2 AL0 BB4 FL1 FM2 Station C RP0 BA0 BB5 FL0 FM0 Station A BB6 BB1 T2 T3 PP1 AL1 FL2 T4 BA1 FM1 Station B BB3 PP2 FL3 BA2 T0 T1 PP3 BB7 PP4 PP5 PP6 PP7 PP8 PP9 PP10 PP11 PP12 branch_b__exit_left_0 (left) prep__exit_right_1 (right) align__exit_right_2 (right) branch_a__exit_right_3 (right) feeder_l1__exit_left_4 (left) feeder_l2__exit_right_5 (right) feeder_l1__entry_right_6 (right) align__entry_left_7 (left) branch_a__entry_left_8 (left) branch_b__entry_right_9 (right) feeder_l2__entry_left_10 (left) target__entry_left_11 (left) report__entry_left_12 (left) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 2 grid row 1 grid row 2 grid __converge_ff2_1 Line 1 Line 2 Line 3 created with nf-metro v1.1.0+dev

Merge & Convergence

Junction Entry Reversed Fold changed

Base (main)

Junction Entry Reversed Fold 1 Bridge 2 Source 3 Dest Alpha 4 Dest Beta Mark Process A Process B Hub Recal Output A Output B tb__exit_right_0 (right) src__exit_right_1 (right) src__entry_left_2 (left) dst_a__entry_left_3 (left) dst_b__entry_left_4 (left) __junction_5 (?) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Alpha Beta created with nf-metro v1.1.0+dev

PR

Junction Entry Reversed Fold 1 Bridge 2 Source 3 Dest Alpha 4 Dest Beta Mark Process A Process B Hub Recal Output A Output B tb__exit_right_0 (right) src__exit_right_1 (right) src__entry_left_2 (left) dst_a__entry_left_3 (left) dst_b__entry_left_4 (left) __junction_5 (?) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Alpha Beta created with nf-metro v1.1.0+dev

Junction Fanout Convergence changed

Base (main)

Junction Fan-out Convergence 1 Caller A 2 Caller B 3 Caller C 4 Joint Calling Merge Call A Call B Call C Collect stepA__exit_right_0 (right) stepB__exit_right_1 (right) stepC__exit_right_2 (right) joint__entry_left_3 (left) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Line A Line B Line C created with nf-metro v1.1.0+dev

PR

Junction Fan-out Convergence 1 Caller A 2 Caller B 3 Caller C 4 Joint Calling Merge Call A Call B Call C Collect stepA__exit_right_0 (right) stepB__exit_right_1 (right) stepC__exit_right_2 (right) joint__entry_left_3 (left) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Line A Line B Line C created with nf-metro v1.1.0+dev

Merge Bottom Row Bypass changed

Base (main)

Bottommost-Row Merge Inter-Row Bypass 1 Fan Source A 2 Fan Source B 3 Side 5 Middle 4 Target In In Side Process Process Out Out Out Out Out src_fanA__exit_right_0 (right) src_fanB__exit_right_1 (right) target__entry_right_2 (right) side_a__entry_left_3 (left) __junction_4 (?) __junction_5 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 1 grid row 2 grid A B created with nf-metro v1.1.0+dev

PR

Bottommost-Row Merge Inter-Row Bypass 1 Fan Source A 2 Fan Source B 3 Side 5 Middle 4 Target In In Side Process Process Out Out Out Out Out src_fanA__exit_right_0 (right) src_fanB__exit_right_1 (right) target__entry_right_2 (right) side_a__entry_left_3 (left) __junction_4 (?) __junction_5 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 1 grid row 2 grid A B created with nf-metro v1.1.0+dev

Merge Feeder Shared Channel Gap changed

Base (main)

Merge feeders sharing a co-located descent channel 1 Fan Source A 6 Left Mate 2 Fan Source B 3 Side 5 Middle 4 Target In In Side Process LM Process Out Out Out Out Out Out src_fanA__exit_right_0 (right) src_fanB__exit_right_1 (right) target__entry_right_2 (right) side_a__entry_left_3 (left) __junction_4 (?) __junction_5 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 1 grid row 1 grid row 0 grid row 1 grid row 2 grid A B created with nf-metro v1.1.0+dev

PR

Merge feeders sharing a co-located descent channel 1 Fan Source A 6 Left Mate 2 Fan Source B 3 Side 5 Middle 4 Target In In Side Process LM Process Out Out Out Out Out Out src_fanA__exit_right_0 (right) src_fanB__exit_right_1 (right) target__entry_right_2 (right) side_a__entry_left_3 (left) __junction_4 (?) __junction_5 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 1|2 row 0 grid row 1 grid row 1 grid row 0 grid row 1 grid row 2 grid A B created with nf-metro v1.1.0+dev

Merge Right Entry changed

Base (main)

Merge Right Entry Cross Row 4 Sink 1 Source 2 Extra 3 Step A Collect Produce Extra Process A Report Prepare Extra Out Out A source__exit_right_0 (right) extra__exit_right_1 (right) step_a__exit_right_2 (right) extra__entry_left_3 (left) sink__entry_right_4 (right) step_a__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) col 0|2 col 2|4 col 4|6 row 0|1 row 0 grid row 1 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

PR

Merge Right Entry Cross Row 4 Sink 1 Source 2 Extra 3 Step A Collect Produce Extra Process A Report Prepare Extra Out Out A source__exit_right_0 (right) extra__exit_right_1 (right) step_a__exit_right_2 (right) extra__entry_left_3 (left) sink__entry_right_4 (right) step_a__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) col 0|2 col 2|4 col 4|6 row 0|1 row 0 grid row 1 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

Feature Showcase

Legend Combo changed

Base (main)

Tumor-Normal Calling FASTQ Alignment FastQC MarkDuplicates MultiQC BQSR Somatic Calling Annotate Tumor Quality Control Tumor-normal pair created with nf-metro v1.1.0+dev

PR

Tumor-Normal Calling FASTQ Alignment FastQC MarkDuplicates MultiQC BQSR Somatic Calling Annotate Tumor Quality Control Tumor-normal pair created with nf-metro v1.1.0+dev

Realistic Pipelines

Longread Variant Calling changed

Base (main)

Long-read Variant Calling 1 Pre-processing 2 Small variant calling 7 CNVs 8 Repeats 3 Phasing 4 Structural Variants 5 Joint Calling 6 Annotation 9 Reports FASTQ BAM uBAM Sniffles WhatsHap Phase CuteSV Clair3 ont-spectre CNVCaller LongTR Jasmine merge samples VEP Geneyx Deepvariant Straglr GLNexus SnpEff SV Report TRGT AnnotSV samtoolsmerge cat FASTQ WhatsHap Haplotag Jasmine merge callers minimap2 samtoolssort/index mosdepth preprocessing__exit_right_0 (right) tr_calling__exit_left_1 (left) small_variants__exit_right_2 (right) phasing__exit_left_3 (left) cnv_calling__exit_left_4 (left) structural_variants__exit_left_5 (left) annotation__exit_left_6 (left) jointcalling__exit_left_7 (left) small_variants__entry_left_8 (left) tr_calling__entry_right_9 (right) cnv_calling__entry_right_10 (right) reports__entry_right_11 (right) phasing__entry_left_12 (left) jointcalling__entry_right_13 (right) annotation__entry_right_14 (right) structural_variants__entry_right_15 (right) __junction_16 (?) __junction_17 (?) __junction_18 (?) __junction_19 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 0 grid row 1 grid row 0 grid uBAM FASTQ BAM Other SNV VCF SV VCF created with nf-metro v1.1.0+dev

PR

Long-read Variant Calling 1 Pre-processing 2 Small variant calling 7 CNVs 8 Repeats 3 Phasing 4 Structural Variants 5 Joint Calling 6 Annotation 9 Reports FASTQ BAM uBAM Sniffles WhatsHap Phase CuteSV Clair3 ont-spectre CNVCaller LongTR Jasmine merge samples VEP Geneyx Deepvariant Straglr GLNexus SnpEff SV Report TRGT AnnotSV samtoolsmerge cat FASTQ WhatsHap Haplotag Jasmine merge callers minimap2 samtoolssort/index mosdepth preprocessing__exit_right_0 (right) tr_calling__exit_left_1 (left) small_variants__exit_right_2 (right) phasing__exit_left_3 (left) cnv_calling__exit_left_4 (left) structural_variants__exit_left_5 (left) annotation__exit_left_6 (left) jointcalling__exit_left_7 (left) small_variants__entry_left_8 (left) tr_calling__entry_right_9 (right) cnv_calling__entry_right_10 (right) reports__entry_right_11 (right) phasing__entry_left_12 (left) jointcalling__entry_right_13 (right) annotation__entry_right_14 (right) structural_variants__entry_right_15 (right) __junction_16 (?) __junction_17 (?) __junction_18 (?) __junction_19 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 0 grid row 1 grid row 0 grid uBAM FASTQ BAM Other SNV VCF SV VCF created with nf-metro v1.1.0+dev

Rowmate Tb Side Entry Top Align changed

Base (main)

TB side-entry row-mate top alignment 1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing FASTQ HTML STAR Picard Bowtie2 HISAT2 Salmon Kallisto cat FASTQ BEDTools UMI-tools Dedup tximport FastQC RSEM bedGraphToBigWig Salmon UMI-tools Extract tximport StringTie fastp Sum. Exp. Trim Galore! FastQC MultiQC BBSplit SortMeRNA RiboDetector Bowtie2 FastQC Infer Strand. preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) genome_align__entry_left_2 (left) pseudo_align__entry_left_3 (left) postprocessing__entry_left_4 (left) __junction_5 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 0 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: Bowtie2 (prokaryotic), Quantification: Salmon Aligner: HISAT2, Quantification: None Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

PR

TB side-entry row-mate top alignment 1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing FASTQ HTML STAR Picard Bowtie2 HISAT2 Salmon Kallisto cat FASTQ BEDTools UMI-tools Dedup tximport FastQC RSEM bedGraphToBigWig Salmon UMI-tools Extract tximport StringTie fastp Sum. Exp. Trim Galore! FastQC MultiQC BBSplit SortMeRNA RiboDetector Bowtie2 FastQC Infer Strand. preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) genome_align__entry_left_2 (left) pseudo_align__entry_left_3 (left) postprocessing__entry_left_4 (left) __junction_5 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 0 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: Bowtie2 (prokaryotic), Quantification: Salmon Aligner: HISAT2, Quantification: None Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

nf-core Pipelines

Pipeline Variantbenchmarking changed

Base (main)

nf-core/variantbenchmarking 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_top_10 (top) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev

PR

nf-core/variantbenchmarking 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_top_10 (top) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev

Inter-section Routing

Plan Owned Distinct Lane Separation changed

Base (main)

Plan-owned distinct lane separation 7 Primary target 2 6 Primary target 5 Secondary target 4 Shared source 3 Secondary near 2 Secondary far 1 Primary far Join Join Join Prepare Near Far Primary source Publish Publish Publish Dispatch primary_far__exit_left_0 (left) secondary_near__exit_left_1 (left) secondary_far__exit_left_2 (left) shared_source__exit_left_3 (left) target_secondary__exit_left_4 (left) target_primary__entry_right_5 (right) target_primary_far__entry_right_6 (right) target_secondary__entry_right_7 (right) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid Primary Secondary Carrier created with nf-metro v1.1.0+dev

PR

Plan-owned distinct lane separation 7 Primary target 2 6 Primary target 5 Secondary target 4 Shared source 3 Secondary near 2 Secondary far 1 Primary far Join Join Join Prepare Near Far Primary source Publish Publish Publish Dispatch primary_far__exit_left_0 (left) secondary_near__exit_left_1 (left) secondary_far__exit_left_2 (left) shared_source__exit_left_3 (left) target_secondary__exit_left_4 (left) target_primary__entry_right_5 (right) target_primary_far__entry_right_6 (right) target_secondary__entry_right_7 (right) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 col 5|6 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid Primary Secondary Carrier created with nf-metro v1.1.0+dev

Basic Topologies

Self Crossing Bridge changed

Base (main)

Self-Crossing Bridge 1 Top 3 Mid Source 4 Mid Sink 2 Bus Sink Top In Mid In Mid Collect Bus Collect Top Out Mid Out Mid Report Bus Report top__exit_right_0 (right) mid_src__exit_right_1 (right) bus_sink__entry_left_2 (left) mid_sink__entry_left_3 (left) col 0|1 row 0|1 row 1|2 row 0 grid row 1 grid row 1 grid row 2 grid Bus created with nf-metro v1.1.0+dev

PR

Self-Crossing Bridge 1 Top 3 Mid Source 4 Mid Sink 2 Bus Sink Top In Mid In Mid Collect Bus Collect Top Out Mid Out Mid Report Bus Report top__exit_right_0 (right) mid_src__exit_right_1 (right) bus_sink__entry_left_2 (left) mid_sink__entry_left_3 (left) col 0|1 row 0|1 row 1|2 row 0 grid row 1 grid row 1 grid row 2 grid Bus created with nf-metro v1.1.0+dev

Guide Examples

Variantbenchmarking changed

Base (main)

nf-core/variantbenchmarking 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_top_10 (top) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev

PR

nf-core/variantbenchmarking 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_top_10 (top) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev

Variantbenchmarking Auto changed

Base (main)

nf-core/variantbenchmarking (auto layout) 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_right_10 (right) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev

PR

nf-core/variantbenchmarking (auto layout) 1 Inputs 2 Preprocessing (Optional) 3 Variant Normalization (Optional) 4 Variant Filtering (Optional) 6 Ensembl Truth 7 Benchmarking 8 Output Processing 5 Variant Statistics FASTA VCF BED BED TSV CSV HTML HTML TSV TSV Subsample SVProcessing FilterContigs bcftoolsstats SURVIVORstats Truvari SVanalyzer bcftoolsfilter RTGtools bndeval Samplesheet SURVIVORmerge SURVIVORfilter wittyer Reference Genome Liftover(Picard, UCSC) VariantNormalization bcftoolsmerge RTGtools vcfeval Truth VCF hap.py Regions BED som.py Targets BED GATK4 Concordance MergeTP/FP/FN SNV stats Intersection SummaryStats SV stats BenchmarkingSummaries ConsensusFilter VCF toCSV datavzrd MergedCSVs Plots HTMLReport MultiQCReport inputs__exit_right_0 (right) preprocess__exit_right_1 (right) normalization__exit_right_2 (right) filtering__exit_right_3 (right) ensembl_truth__exit_left_4 (left) benchmarking__exit_left_5 (left) preprocess__entry_left_6 (left) normalization__entry_left_7 (left) filtering__entry_left_8 (left) stats__entry_left_9 (left) ensembl_truth__entry_right_10 (right) benchmarking__entry_right_11 (right) output_processing__entry_right_12 (right) __junction_13 (?) __junction_14 (?) __junction_15 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 1 grid _inputs_hub _ensembl_hub Test Preprocessing Truth Preprocessing SV/CNV Benchmarking SNV/INDEL Benchmarking Concordance Intersection Output Processing created with nf-metro v1.1.0+dev