70 changed out of 312 total renders. Generated 2026-08-07 20:43 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
03b_fan_in_merge0000.6140.9074.1→79.1 (+5.0)064%
variantbenchmarking3001.0961.2037.6715%
variantbenchmarking_auto4001.0961.2037.6515%
bypass_fan_in_outer_slot4000.3220.4063.7→58.8 (−4.8)042%→42% (+0%)
bypass_leftward_far_side_entry0000.8281.2070.1071%→72% (+1%)
convergent_offrow_exit_climb13001.2841.5028.0140%→41% (+1%)
disjoint_sameline_trunks6→4 (−2)000.7161.0076.0066%
dogleg_exempt_distinct0000.9121.4060.1048%→48% (+1%)
dogleg_exempt_sameline0000.981.40–→n/a044%→45% (+1%)
fold_bypass_creep0000.7130.9028.5141%
fold_bypass_creep_tight0000.8131.0028.5142%
same_line_fan_distinct_descent7→5 (−2)000.6120.9084.0→76.0 (−8.0)038%→38% (+0%)
compact_gap_peer_conflict0000.140.1→0.1 (−0.0)035.0→36.0 (+1.0)065%
exit_run_three_drop_columns5000.3→0.3 (+0.0)130.5→0.5 (+0.0)060.1047%
multi_frame_exit_lane_settlement1000.3260.50110.8→81.2 (−29.5)046%
complex_multipath3000.3160.4073.0→70.0 (−3.0)051%→52% (+0%)
convergence_stacked_sink0000.5120.70–→n/a036%→37% (+0%)
fanin_distant_terminus0001.0→1.2 (+0.2)10→12 (+2)1.1→1.4 (+0.4)0–→n/a152%→47% (−5%)
merge_adjacent_feeder2001.2201.4074.1147%
merge_around_below_leftmost0000.7101.10–→n/a043%
merge_bottom_row_bypass0000.5→0.5 (+0.0)80.8→0.8 (+0.1)076.0038%
merge_feeder_shared_channel_gap0000.5→0.5 (+0.0)80.7→0.8 (+0.0)076.0037%
merge_feeders_three_columns2000.290.4060.1049%
merge_leftmost_sink_branch0000.360.50–→n/a042%
merge_pullaway0000.460.60–→n/a046%
merge_right_entry0000.6100.90–→n/a044%→43% (−0%)
merge_trunk_out_of_range_section0000.8→0.8 (+0.0)141.2→1.3 (+0.1)0–→n/a044%
merge_trunk_over_low_section0000.7160.9074.1→82.1 (+8.0)042%
cross_row_gap_wrap0000.490.6080.1043%
multicarrier_offrow_exit_climb2000.9181.2039.0048%
orbit_perp_exit_back_row_entry0000.580.80–→n/a050%
diagonal_labels0000.4200.6064.0235%
multi_section_cell0000.120.10–→n/a046%
multirow_source_stacked_fan0000.6200.7→0.7 (+0.0)039.2→51.9 (+12.7)136%
peeloff_straight_drop_near_wall1000.340.4066.0050%
straight_drop_below0000.540.80100.0056%
top_entry_left_neighbour0000.961.20–→n/a049%
differentialabundance33001.31801.4046.4518%→18% (+0%)
differentialabundance_default53001.11561.4046.4216%→16% (+0%)
genomeassembly_staggered6001.1581.4036.0115%
genomic_pipeline27001.32761.7035.0312%
longread_variant_calling15001.3951.7028.0121%→22% (+0%)
fan_branch_additional_outputs0001.1361.1016.0049%
funcprofiler_upstream35011.2→1.2 (+0.0)981.5→1.5 (+0.0)039.0155%
internal_source_equal_sibling_2fan0001.381.20–→n/a146%
port_fed_three_branch_diamond0000.780.6036.0065%→64% (−1%)
ported_symmetric_fan_centreline_trunk0001.3241.30–→n/a047%
symmetric_deadend_fanout0000.740.50–→n/a066%
terminal_symmetric_fan0000.780.60–→n/a061%
trunk_through_fan0000.7→0.4 (−0.4)16→8 (−8)0.7→0.3 (−0.3)0–→n/a1→0 (−1)57%→63% (+6%)
fold_fan_across0000.3260.4071.1→73.1 (+2.0)033%
fold_stacked_branch2000.2160.3076.1→76.6 (+0.5)029%
opposing_bypass_corridor1000.6161.0080.0047%
packed_cell_right_exit_left_entry_wrap8001.3881.6043.4018%
packed_multiline_serpentine_grid6000.71140.8060.0218%
reconverge_reversed_fold2000.2160.3076.1→76.6 (+0.5)029%
genomeassembly_organellar8000.9→0.9 (+0.0)501.1→1.1 (+0.0)039.0023%
target_entry_runway_bypass13000.81261.0060.0126%
tb_exit_terminal_on_carrier0000.9331.2062.4132%→33% (+1%)
nf_variant_calling_tuned0000.9201.0040.0154%
nf_variant_calling_tuned_icons0000.9241.0036.0152%
off_track_input_above_consumer6000.4280.5058.4028%→28% (+0%)
pipeline_genomeassembly6000.9→0.9 (+0.0)461.1→1.1 (+0.0)039.0056%
pipeline_variantbenchmarking3001.0961.2037.6715%
pipeline_variantprioritization0000.5160.6060.1241%
right_entry_over_top_tall_upstream0000.5120.70–→n/a040%→41% (+1%)
tb_internal_diagonal0000.8101.20–→n/a154%
tb_lr_exit_left0000.580.80–→n/a050%
tb_lr_exit_right0000.8121.20–→n/a055%
self_crossing_bridge0000.440.60–→n/a040%

Changed renders

Guide Examples

Bypass Routing

Multi-line Bundles

Branching and Multipath

Merge & Convergence

Inter-section Routing

Feature Showcase

Realistic Pipelines

Fan-out and Fan-in

Serpentine Layout

Test Fixtures

Nextflow Conversions

Off-track & Rails

nf-core Pipelines

TB / BT Sections

Basic Topologies

Guide Examples

03B Fan In Merge changed

Base (main)

Fan-In Merge 1 2 3 4 Produce Process A Process B Collect Prepare Refine A Refine B Report source__exit_right_0 (right) step_a__exit_right_1 (right) step_b__exit_right_2 (right) step_a__entry_left_3 (left) step_b__entry_left_4 (left) sink__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Main Auxiliary created with nf-metro v1.1.0+dev

PR

Fan-In Merge 1 2 3 4 Produce Process A Process B Collect Prepare Refine A Refine B Report source__exit_right_0 (right) step_a__exit_right_1 (right) step_b__exit_right_2 (right) step_a__entry_left_3 (left) step_b__entry_left_4 (left) sink__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 row 0 grid row 0 grid row 0 grid row 0 grid Main Auxiliary created with nf-metro v1.1.0+dev

Variantbenchmarking changed

Base (main)

nf-core/variantbenchmarking 1 2 3 4 6 7 8 5 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 2 3 4 6 7 8 5 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 2 3 4 6 7 8 5 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 2 3 4 6 7 8 5 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

Bypass Routing

Bypass Fan In Outer Slot changed

Base (main)

Bypass Fan-in Outer Slot 1 2 3 4 5 6 7 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 2 3 4 5 6 7 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 3 2 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 3 2 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

Convergent Offrow Exit Climb changed

Base (main)

Long-read Variant Calling 1 2 5 3 4 6 7 8 9 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 2 5 3 4 6 7 8 9 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 2 3 4 5 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 2 3 4 5 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 2 4 1 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 2 4 1 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

Dogleg Exempt Sameline changed

Base (main)

Dogleg Off Exempt Trunks - Same Line Regime 2 1 3 Collect Input R Hub N Output Hub R Out N right_src__exit_right_0 (right) left_tgt__exit_right_1 (right) left_tgt__entry_left_2 (left) new_tgt__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 1 grid Wrap created with nf-metro v1.1.0+dev

PR

Dogleg Off Exempt Trunks - Same Line Regime 2 1 3 Collect Input R Hub N Output Hub R Out N right_src__exit_right_0 (right) left_tgt__exit_right_1 (right) left_tgt__entry_left_2 (left) new_tgt__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid row 1 grid Wrap created with nf-metro v1.1.0+dev

Fold Bypass Creep changed

Base (main)

Fold Bypass Creep 1 2 3 VCF Caller A CallerB MultiQC Align Stats prep__exit_right_0 (right) calling__exit_left_1 (left) calling__entry_left_2 (left) report__entry_right_3 (right) __junction_4 (?) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid __bypass_collate_stats_1 __bypass_vcf_out_stats_2 Main QC created with nf-metro v1.1.0+dev

PR

Fold Bypass Creep 1 2 3 VCF Caller A CallerB MultiQC Align Stats prep__exit_right_0 (right) calling__exit_left_1 (left) calling__entry_left_2 (left) report__entry_right_3 (right) __junction_4 (?) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid __bypass_collate_stats_1 __bypass_vcf_out_stats_2 Main QC created with nf-metro v1.1.0+dev

Fold Bypass Creep Tight changed

Base (main)

Fold Bypass Creep (tight) 1 2 3 VCF Caller A CallerB MultiQC Align Stats prep__exit_right_0 (right) calling__exit_left_1 (left) calling__entry_left_2 (left) report__entry_right_3 (right) __junction_4 (?) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid __bypass_vcf_out_stats_1 Main QC created with nf-metro v1.1.0+dev

PR

Fold Bypass Creep (tight) 1 2 3 VCF Caller A CallerB MultiQC Align Stats prep__exit_right_0 (right) calling__exit_left_1 (left) calling__entry_left_2 (left) report__entry_right_3 (right) __junction_4 (?) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid __bypass_vcf_out_stats_1 Main QC created with nf-metro v1.1.0+dev

Same Line Fan Distinct Descent changed

Base (main)

Same-line fan with distinct descent 1 2 3 4 5 Input Carry on FarStep NearStep MidStep Process src__exit_right_0 (right) cont__entry_left_1 (left) far__entry_top_2 (top) near__entry_left_3 (left) mid__entry_left_4 (left) __junction_5 (?) 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 3 grid Red Green Blue created with nf-metro v1.1.0+dev

PR

Same-line fan with distinct descent 1 2 3 4 5 Input Carry on FarStep NearStep MidStep Process src__exit_right_0 (right) cont__entry_left_1 (left) far__entry_top_2 (top) near__entry_left_3 (left) mid__entry_left_4 (left) __junction_5 (?) 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 3 grid Red Green Blue created with nf-metro v1.1.0+dev

Multi-line Bundles

Compact Gap Peer Conflict changed

Base (main)

Compaction Gap Peer Conflict 1 2 3 Input Fork End Prepare Alpha Gamma Beta Node Merge src__exit_right_0 (right) proc__exit_right_1 (right) proc__entry_left_2 (left) sink__entry_left_3 (left) col 0|1 col 1|2 row 0 grid Alpha Beta Gamma created with nf-metro v1.1.0+dev

PR

Compaction Gap Peer Conflict 1 2 3 Input Fork End Prepare Alpha Gamma Beta Node Merge src__exit_right_0 (right) proc__exit_right_1 (right) proc__entry_left_2 (left) sink__entry_left_3 (left) col 0|1 col 1|2 row 0 grid Alpha Beta Gamma created with nf-metro v1.1.0+dev

Exit Run Three Drop Columns changed

Base (main)

Exit run, three drop columns 1 2 3 4 5 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 2 3 4 5 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

Multi Frame Exit Lane Settlement changed

Base (main)

Independent Exit Lane Frames 1 2 3 4 5 12 11 6 7 8 9 10 13 14 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 2 3 4 5 12 11 6 7 8 9 10 13 14 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

Branching and Multipath

Complex Multipath changed

Base (main)

Complex Multipath 1 2 3 5 4 6 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 2 3 5 4 6 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

Merge & Convergence

Convergence Stacked Sink changed

Base (main)

Convergence Stacked Sink 1 4 2 5 3 6 7 Input Load Map Detect Mark Combine Summarise Output Index Sort Genotype Recal Refine Publish prep__exit_right_0 (right) aux__exit_right_1 (right) align__exit_right_2 (right) dedup__exit_right_3 (right) repeats__exit_left_4 (left) merge_pt__exit_left_5 (left) align__entry_left_6 (left) repeats__entry_right_7 (right) dedup__entry_left_8 (left) merge_pt__entry_right_9 (right) report__entry_right_10 (right) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid row 0 grid row 2 grid row 2 grid Main created with nf-metro v1.1.0+dev

PR

Convergence Stacked Sink 1 4 2 5 3 6 7 Input Load Map Detect Mark Combine Summarise Output Index Sort Genotype Recal Refine Publish prep__exit_right_0 (right) aux__exit_right_1 (right) align__exit_right_2 (right) dedup__exit_right_3 (right) repeats__exit_left_4 (left) merge_pt__exit_left_5 (left) align__entry_left_6 (left) repeats__entry_right_7 (right) dedup__entry_left_8 (left) merge_pt__entry_right_9 (right) report__entry_right_10 (right) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid row 0 grid row 2 grid row 2 grid Main created with nf-metro v1.1.0+dev

Fanin Distant Terminus changed

Base (main)

Fan-in to a distant terminus 1 HTML Report Prep anota2seq deltaTE DOTSeq ORFquant ORFtest row 0 grid __converge_report_1 __converge_report_2 Line A created with nf-metro v1.1.0+dev

PR

Fan-in to a distant terminus 1 HTML Report Prep anota2seq deltaTE DOTSeq ORFquant ORFtest row 0 grid __converge_report_1 __converge_report_2 Line A created with nf-metro v1.1.0+dev

Merge Adjacent Feeder changed

Base (main)

Merge Adjacent Feeder 1 2 3 4 Score Produce Collect Summarise Plot Filter source__exit_right_0 (right) middle__exit_right_1 (right) middle__entry_left_2 (left) report__entry_left_3 (left) sink__entry_left_4 (left) __junction_5 (?) __junction_6 (?) __merge_2 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid Main Side created with nf-metro v1.1.0+dev

PR

Merge Adjacent Feeder 1 2 3 4 Score Produce Collect Summarise Plot Filter source__exit_right_0 (right) middle__exit_right_1 (right) middle__entry_left_2 (left) report__entry_left_3 (left) sink__entry_left_4 (left) __junction_5 (?) __junction_6 (?) __merge_2 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid Main Side created with nf-metro v1.1.0+dev

Merge Around Below Leftmost changed

Base (main)

Merge Around Below Leftmost 1 2 3 4 Step A Step B Extra Step Combine Out A Out B Extra Out Result src1__exit_right_0 (right) src2__exit_right_1 (right) extra__entry_left_2 (left) tgt__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 0 grid row 0 grid row 0 grid row 1 grid A created with nf-metro v1.1.0+dev

PR

Merge Around Below Leftmost 1 2 3 4 Step A Step B Extra Step Combine Out A Out B Extra Out Result src1__exit_right_0 (right) src2__exit_right_1 (right) extra__entry_left_2 (left) tgt__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 0 grid row 0 grid row 0 grid row 1 grid A created with nf-metro v1.1.0+dev

Merge Bottom Row Bypass changed

Base (main)

Bottommost-Row Merge Inter-Row Bypass 1 2 3 5 4 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 2 3 5 4 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 6 2 3 5 4 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 6 2 3 5 4 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 Feeders Three Columns changed

Base (main)

Report feeders from three columns 1 2 3 4 5 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 (?) 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

Report feeders from three columns 1 2 3 4 5 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 (?) 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

Merge Leftmost Sink Branch changed

Base (main)

Merge Leftmost Sink Branch 1 2 3 4 5 Block Start Process A Process B Extra Collect Block End Out A Out B Extra Out Report blocker__exit_right_0 (right) step_a__exit_right_1 (right) step_b__exit_right_2 (right) step_a__entry_left_3 (left) step_b__entry_left_4 (left) sink__entry_left_5 (left) extra__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __merge_2 (?) col 0|1 col 1|3 col 3|5 col 5|6 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid A created with nf-metro v1.1.0+dev

PR

Merge Leftmost Sink Branch 1 2 3 4 5 Block Start Process A Process B Extra Collect Block End Out A Out B Extra Out Report blocker__exit_right_0 (right) step_a__exit_right_1 (right) step_b__exit_right_2 (right) step_a__entry_left_3 (left) step_b__entry_left_4 (left) sink__entry_left_5 (left) extra__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __merge_2 (?) col 0|1 col 1|3 col 3|5 col 5|6 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid A created with nf-metro v1.1.0+dev

Merge Pullaway changed

Base (main)

Merge trunk pull-away cross-row sibling 1 2 3 4 5 Start Block Step Side Merge Out Pass Done Out Report wide_src__exit_right_0 (right) sibling_sec__exit_right_1 (right) obstacle__entry_left_2 (left) target__entry_left_3 (left) side_dst__entry_left_4 (left) __junction_5 (?) __junction_6 (?) __merge_2 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid row 0 grid Main created with nf-metro v1.1.0+dev

PR

Merge trunk pull-away cross-row sibling 1 2 3 4 5 Start Block Step Side Merge Out Pass Done Out Report wide_src__exit_right_0 (right) sibling_sec__exit_right_1 (right) obstacle__entry_left_2 (left) target__entry_left_3 (left) side_dst__entry_left_4 (left) __junction_5 (?) __junction_6 (?) __merge_2 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid row 0 grid Main created with nf-metro v1.1.0+dev

Merge Right Entry changed

Base (main)

Merge Right Entry Cross Row 4 1 2 3 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 1 2 3 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

Merge Trunk Out Of Range Section changed

Base (main)

Merge Trunk Out-of-Range Section 1 2 3 4 5 6 Merge Far Mid Step Near Extra Step Other Report mid__exit_right_0 (right) src_far__exit_right_1 (right) src_near__exit_right_2 (right) extra__exit_right_3 (right) src_near__entry_left_4 (left) sink__entry_left_5 (left) extra__entry_left_6 (left) other__entry_top_7 (top) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid Main created with nf-metro v1.1.0+dev

PR

Merge Trunk Out-of-Range Section 1 2 3 4 5 6 Merge Far Mid Step Near Extra Step Other Report mid__exit_right_0 (right) src_far__exit_right_1 (right) src_near__exit_right_2 (right) extra__exit_right_3 (right) src_near__entry_left_4 (left) sink__entry_left_5 (left) extra__entry_left_6 (left) other__entry_top_7 (top) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) col 0|1 col 1|2 col 2|3 col 3|4 col 4|5 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid Main created with nf-metro v1.1.0+dev

Merge Trunk Over Low Section changed

Base (main)

Merge Trunk Over Low Section 1 2 3 4 5 Read Branch Gather Aux Step Path A Split Path B Report Done Path C ingest__exit_right_0 (right) tall__exit_right_1 (right) proc2__exit_right_2 (right) tall__entry_left_3 (left) collect__entry_left_4 (left) proc2__entry_left_5 (left) sub__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __merge_2 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid Flow Side created with nf-metro v1.1.0+dev

PR

Merge Trunk Over Low Section 1 2 3 4 5 Read Branch Gather Aux Step Path A Split Path B Report Done Path C ingest__exit_right_0 (right) tall__exit_right_1 (right) proc2__exit_right_2 (right) tall__entry_left_3 (left) collect__entry_left_4 (left) proc2__entry_left_5 (left) sub__entry_left_6 (left) __junction_7 (?) __junction_8 (?) __merge_2 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid Flow Side created with nf-metro v1.1.0+dev

Inter-section Routing

Cross Row Gap Wrap changed

Base (main)

Cross-Row Gap Wrap 1 2 3 4 5 Read Map Mark Combine Summarise QC Sort Recal Refine Publish ingest__exit_right_0 (right) align__exit_right_1 (right) dedup__exit_bottom_2 (bottom) merge_pt__exit_left_3 (left) align__entry_left_4 (left) dedup__entry_left_5 (left) merge_pt__entry_top_6 (top) report__entry_right_7 (right) __junction_8 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid Main Feed created with nf-metro v1.1.0+dev

PR

Cross-Row Gap Wrap 1 2 3 4 5 Read Map Mark Combine Summarise QC Sort Recal Refine Publish ingest__exit_right_0 (right) align__exit_right_1 (right) dedup__exit_bottom_2 (bottom) merge_pt__exit_left_3 (left) align__entry_left_4 (left) dedup__entry_left_5 (left) merge_pt__entry_top_6 (top) report__entry_right_7 (right) __junction_8 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid Main Feed created with nf-metro v1.1.0+dev

Multicarrier Offrow Exit Climb changed

Base (main)

Multi-carrier off-row exit climb 1 2 3 FASTQ BAM uBAM Clair3 LongTR Deepvariant ont-spectre samtoolsmerge cat FASTQ minimap2 samtoolssort/index mosdepth prep__exit_right_0 (right) variants__entry_left_1 (left) depth__entry_left_2 (left) __junction_3 (?) col 0|1 row 0|1 row 0 grid row 1 grid uBAM FASTQ BAM Other created with nf-metro v1.1.0+dev

PR

Multi-carrier off-row exit climb 1 2 3 FASTQ BAM uBAM Clair3 LongTR Deepvariant ont-spectre samtoolsmerge cat FASTQ minimap2 samtoolssort/index mosdepth prep__exit_right_0 (right) variants__entry_left_1 (left) depth__entry_left_2 (left) __junction_3 (?) col 0|1 row 0|1 row 0 grid row 1 grid uBAM FASTQ BAM Other created with nf-metro v1.1.0+dev

Orbit Perp Exit Back Row Entry changed

Base (main)

Orbit - Perp Exit, Row Behind 1 2 3 Stage Compute Store Check Reduce prepare__exit_right_0 (right) process__exit_left_1 (left) process__entry_top_2 (top) archive__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid A B created with nf-metro v1.1.0+dev

PR

Orbit - Perp Exit, Row Behind 1 2 3 Stage Compute Store Check Reduce prepare__exit_right_0 (right) process__exit_left_1 (left) process__entry_top_2 (top) archive__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid A B created with nf-metro v1.1.0+dev

Feature Showcase

Diagonal Labels changed

Base (main)

Diagonal Labels (dense trunk) 1 2 FASTQ VCF split by analysis FastQC GATK Mutect2 Strelka2 FastP merge VCFs UMI consensus BWA-MEM samtools merge/index MarkDuplicates BaseRecalibrator ApplyBQSR mosdepth NGSCheckmate preprocessing__exit_right_0 (right) variant_calling__entry_left_1 (left) row 0|1 row 0 grid row 1 grid Germline Tumor only Tumor-normal pair created with nf-metro v1.1.0+dev

PR

Diagonal Labels (dense trunk) 1 2 FASTQ VCF split by analysis FastQC GATK Mutect2 Strelka2 FastP merge VCFs UMI consensus BWA-MEM samtools merge/index MarkDuplicates BaseRecalibrator ApplyBQSR mosdepth NGSCheckmate preprocessing__exit_right_0 (right) variant_calling__entry_left_1 (left) row 0|1 row 0 grid row 1 grid Germline Tumor only Tumor-normal pair created with nf-metro v1.1.0+dev

Multi Section Cell changed

Base (main)

Multi-section cell packing 1 2 4 5 3 6 7 Input Call Pileup Norm Index Report Consensus Trim Filter Genotype Annotate Realign Summary Final Phase Dedup Recal BQSR Score Merge Emit Sort pre__exit_right_0 (right) short_a__exit_right_1 (right) long_a__exit_right_2 (right) long_b__exit_right_3 (right) short_b__exit_right_4 (right) short_a__entry_left_5 (left) long_a__entry_left_6 (left) norm__entry_left_7 (left) long_b__entry_left_8 (left) short_b__entry_left_9 (left) cons__entry_left_10 (left) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

PR

Multi-section cell packing 1 2 4 5 3 6 7 Input Call Pileup Norm Index Report Consensus Trim Filter Genotype Annotate Realign Summary Final Phase Dedup Recal BQSR Score Merge Emit Sort pre__exit_right_0 (right) short_a__exit_right_1 (right) long_a__exit_right_2 (right) long_b__exit_right_3 (right) short_b__exit_right_4 (right) short_a__entry_left_5 (left) long_a__entry_left_6 (left) norm__entry_left_7 (left) long_b__entry_left_8 (left) short_b__entry_left_9 (left) cons__entry_left_10 (left) __junction_11 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

Multirow Source Stacked Fan changed

Base (main)

Multi-row source, stacked fan 1 2 3 4 FASTQ Reads sambamba markdup RSEM Arriba STAR-Fusion flagstat + mosdepth BBDuk trim RNA-SeQC Gene annotation Merge fusions STAR 2-pass Draw fusions samtools CRAM align_sec__exit_right_0 (right) qc_sec__entry_left_1 (left) quant_sec__entry_left_2 (left) fusion_sec__entry_left_3 (left) __junction_4 (?) col 0|1 row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid __bypass_cram_star_1 Alignment QC Quantification Fusion detection created with nf-metro v1.1.0+dev

PR

Multi-row source, stacked fan 1 2 3 4 FASTQ Reads sambamba markdup RSEM Arriba STAR-Fusion flagstat + mosdepth BBDuk trim RNA-SeQC Gene annotation Merge fusions STAR 2-pass Draw fusions samtools CRAM align_sec__exit_right_0 (right) qc_sec__entry_left_1 (left) quant_sec__entry_left_2 (left) fusion_sec__entry_left_3 (left) __junction_4 (?) col 0|1 row 0|1 row 1|2 row 0 grid row 1 grid row 2 grid __bypass_cram_star_1 Alignment QC Quantification Fusion detection created with nf-metro v1.1.0+dev

Peeloff Straight Drop Near Wall changed

Base (main)

Peel-off Straight Drop Near Wall 1 2 3 4 5 Trim Align Quantify TE Assemble preprocessing__exit_right_0 (right) alignment__exit_right_1 (right) quantification__exit_right_2 (right) alignment__entry_left_3 (left) quantification__entry_left_4 (left) novel_transcripts__entry_top_5 (top) te__entry_right_6 (right) __junction_7 (?) col 0|1 row 0|1 row 1|2 row 0 grid row 0 grid row 0 grid row 1 grid row 2 grid Ribo RNA created with nf-metro v1.1.0+dev

PR

Peel-off Straight Drop Near Wall 1 2 3 4 5 Trim Align Quantify TE Assemble preprocessing__exit_right_0 (right) alignment__exit_right_1 (right) quantification__exit_right_2 (right) alignment__entry_left_3 (left) quantification__entry_left_4 (left) novel_transcripts__entry_top_5 (top) te__entry_right_6 (right) __junction_7 (?) col 0|1 row 0|1 row 1|2 row 0 grid row 0 grid row 0 grid row 1 grid row 2 grid Ribo RNA created with nf-metro v1.1.0+dev

Straight Drop Below changed

Base (main)

Straight Drop Below 1 2 3 Source Assemble Collect top__exit_right_0 (right) bottom__entry_top_1 (top) sink__entry_left_2 (left) __junction_3 (?) col 0|1 row 0|1 row 0 grid row 1 grid row 1 grid Main Branch created with nf-metro v1.1.0+dev

PR

Straight Drop Below 1 2 3 Source Assemble Collect top__exit_right_0 (right) bottom__entry_top_1 (top) sink__entry_left_2 (left) __junction_3 (?) col 0|1 row 0|1 row 0 grid row 1 grid row 1 grid Main Branch created with nf-metro v1.1.0+dev

Top Entry Left Neighbour changed

Base (main)

Top Entry Fed From Left Neighbour 1 2 3 4 Ref Load Filter Analyse Prep intake__exit_right_0 (right) producer__exit_right_1 (right) screen__entry_left_2 (left) consumer__entry_top_3 (top) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

PR

Top Entry Fed From Left Neighbour 1 2 3 4 Ref Load Filter Analyse Prep intake__exit_right_0 (right) producer__exit_right_1 (right) screen__entry_left_2 (left) consumer__entry_top_3 (top) col 0|1 col 1|2 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid Main created with nf-metro v1.1.0+dev

Realistic Pipelines

Differentialabundance changed

Base (main)

1 2 3 5 4 YAML Contrasts CSV Samples TSV Matrix GTF GTF CEL Affy CEL TSV MaxQuant STR GEO ID GMT Gene sets TSV Network HTML Shiny HTML Report ZIP Bundle PNG Plots shinyngs Exploratory limma Quarto report Differential DESeq2 dream propd gprofiler2 grea GSEA Annotate results Zip bundle decoupler GTF to table affy load proteus GEOquery Validate Filter matrix data_prep__exit_right_0 (right) differential__exit_right_1 (right) functional__exit_right_2 (right) differential__entry_left_3 (left) functional__entry_left_4 (left) plots__entry_left_5 (left) reporting__entry_left_6 (left) __junction_7 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid __converge_plots_png_1 __bypass_annotate_limma_1 RNA-seq counts Affymetrix microarray MaxQuant proteomics GEO SOFT file created with nf-metro v1.1.0+dev

PR

1 2 3 5 4 YAML Contrasts CSV Samples TSV Matrix GTF GTF CEL Affy CEL TSV MaxQuant STR GEO ID GMT Gene sets TSV Network HTML Shiny HTML Report ZIP Bundle PNG Plots shinyngs Exploratory limma Quarto report Differential DESeq2 dream propd gprofiler2 grea GSEA Annotate results Zip bundle decoupler GTF to table affy load proteus GEOquery Validate Filter matrix data_prep__exit_right_0 (right) differential__exit_right_1 (right) functional__exit_right_2 (right) differential__entry_left_3 (left) functional__entry_left_4 (left) plots__entry_left_5 (left) reporting__entry_left_6 (left) __junction_7 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid __converge_plots_png_1 __bypass_annotate_limma_1 RNA-seq counts Affymetrix microarray MaxQuant proteomics GEO SOFT file created with nf-metro v1.1.0+dev

Differentialabundance Default changed

Base (main)

1 2 3 5 4 YAML Contrasts CSV Samples TSV Matrix GTF GTF CEL Affy CEL TSV MaxQuant STR GEO ID GMT Gene sets TSV Network HTML Shiny HTML Report ZIP Bundle PNG Plots shinyngs Exploratory limma Quarto report Differential DESeq2 dream propd gprofiler2 grea GSEA Annotate results Zip bundle decoupler GTF to table affy load proteus GEOquery Validate Filter matrix data_prep__exit_right_0 (right) differential__exit_right_1 (right) functional__exit_right_2 (right) differential__entry_left_3 (left) functional__entry_left_4 (left) plots__entry_left_5 (left) reporting__entry_left_6 (left) __junction_7 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid __converge_plots_png_1 __bypass_annotate_limma_1 RNA-seq counts Affymetrix microarray MaxQuant proteomics GEO SOFT file created with nf-metro v1.1.0+dev

PR

1 2 3 5 4 YAML Contrasts CSV Samples TSV Matrix GTF GTF CEL Affy CEL TSV MaxQuant STR GEO ID GMT Gene sets TSV Network HTML Shiny HTML Report ZIP Bundle PNG Plots shinyngs Exploratory limma Quarto report Differential DESeq2 dream propd gprofiler2 grea GSEA Annotate results Zip bundle decoupler GTF to table affy load proteus GEOquery Validate Filter matrix data_prep__exit_right_0 (right) differential__exit_right_1 (right) functional__exit_right_2 (right) differential__entry_left_3 (left) functional__entry_left_4 (left) plots__entry_left_5 (left) reporting__entry_left_6 (left) __junction_7 (?) col 0|1 col 1|2 col 2|3 row 0|1 row 0 grid row 1 grid __converge_plots_png_1 __bypass_annotate_limma_1 RNA-seq counts Affymetrix microarray MaxQuant proteomics GEO SOFT file created with nf-metro v1.1.0+dev

Genomeassembly Staggered changed

Base (main)

sanger-tol/genomeassembly 1 2 3 4 5 FASTX CRAM FASTQ bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO hifiasm 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) __junction_8 (?) __junction_9 (?) __junction_10 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|2 col 2|4 col 4|6 col 6|8 row 0 grid row 2 grid row 4 grid row 6 grid row 8 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

PR

sanger-tol/genomeassembly 1 2 3 4 5 FASTX CRAM FASTQ bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO hifiasm 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) __junction_8 (?) __junction_9 (?) __junction_10 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|2 col 2|4 col 4|6 col 6|8 row 0 grid row 2 grid row 4 grid row 6 grid row 8 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

Genomic Pipeline changed

Base (main)

Variant Calling Pipeline 1 2 3 4 5 FASTQ BAM CRAM VCF HTML MultiQC Filter VCFs snpEff FastQC HaplotypeCaller Normalize VEP FastP DeepVariant Sentieon DNAscope Sentieon Haplotyper FreeBayes Strelka bcftools mpileup Manta TIDDIT CNVkit indexcov Mutect2 LoFreq Sentieon TNscope Control-FREEC MSIsensor2 MuSE ASCAT MSIsensor-pro Concatenate bcftools annotate UMI consensus BWA-MEM Consensus SnpSift BWA-MEM2 DragMap Sentieon BWA samtools merge/index Varlociraptor MarkDuplicates bcftools stats Sentieon Dedup BaseRecalibrator VCFtools ApplyBQSR mosdepth NGSCheckmate preprocessing__exit_right_0 (right) variant_calling__exit_right_1 (right) post_vc__exit_right_2 (right) annotation__exit_right_3 (right) variant_calling__entry_left_4 (left) post_vc__entry_left_5 (left) annotation__entry_left_6 (left) reporting__entry_left_7 (left) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) __merge_4 (?) col 0|1 row 0|1 row 1|2 row 2|3 row 1 grid row 0 grid row 2 grid row 3 grid Germline Tumor only Tumor-normal pair created with nf-metro v1.1.0+dev

PR

Variant Calling Pipeline 1 2 3 4 5 FASTQ BAM CRAM VCF HTML MultiQC Filter VCFs snpEff FastQC HaplotypeCaller Normalize VEP FastP DeepVariant Sentieon DNAscope Sentieon Haplotyper FreeBayes Strelka bcftools mpileup Manta TIDDIT CNVkit indexcov Mutect2 LoFreq Sentieon TNscope Control-FREEC MSIsensor2 MuSE ASCAT MSIsensor-pro Concatenate bcftools annotate UMI consensus BWA-MEM Consensus SnpSift BWA-MEM2 DragMap Sentieon BWA samtools merge/index Varlociraptor MarkDuplicates bcftools stats Sentieon Dedup BaseRecalibrator VCFtools ApplyBQSR mosdepth NGSCheckmate preprocessing__exit_right_0 (right) variant_calling__exit_right_1 (right) post_vc__exit_right_2 (right) annotation__exit_right_3 (right) variant_calling__entry_left_4 (left) post_vc__entry_left_5 (left) annotation__entry_left_6 (left) reporting__entry_left_7 (left) __junction_8 (?) __junction_9 (?) __merge_2 (?) __merge_3 (?) __merge_4 (?) col 0|1 row 0|1 row 1|2 row 2|3 row 1 grid row 0 grid row 2 grid row 3 grid Germline Tumor only Tumor-normal pair created with nf-metro v1.1.0+dev

Longread Variant Calling changed

Base (main)

Long-read Variant Calling 1 2 7 8 3 4 5 6 9 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 2 7 8 3 4 5 6 9 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

Fan-out and Fan-in

Fan Branch Additional Outputs changed

Base (main)

Fan Branches with Additional Outputs 1 2 3 Identify taxon Generate reports OMA online OMA local PANTHER online PANTHER local OrthoInspector online EggNOG local input__exit_right_0 (right) fetch_orthologs__exit_right_1 (right) fetch_orthologs__entry_left_2 (left) reporting__entry_left_3 (left) col 0|1 col 1|2 row 0 grid __bypass_join_eggnog_local_1 __bypass_join_inspector_online_2 __bypass_join_oma_local_3 __bypass_join_oma_online_4 __bypass_join_panther_local_5 __bypass_join_panther_online_6 Main flow Report flow created with nf-metro v1.1.0+dev

PR

Fan Branches with Additional Outputs 1 2 3 Identify taxon Generate reports OMA online OMA local PANTHER online PANTHER local OrthoInspector online EggNOG local input__exit_right_0 (right) fetch_orthologs__exit_right_1 (right) fetch_orthologs__entry_left_2 (left) reporting__entry_left_3 (left) col 0|1 col 1|2 row 0 grid __bypass_join_eggnog_local_1 __bypass_join_inspector_online_2 __bypass_join_oma_local_3 __bypass_join_oma_online_4 __bypass_join_panther_local_5 __bypass_join_panther_online_6 Main flow Report flow created with nf-metro v1.1.0+dev

Funcprofiler Upstream changed

Base (main)

nf-core/funcprofiler (upstream) 1 2 3 4 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 2 3 4 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

Internal Source Equal Sibling 2Fan changed

Base (main)

Internal-source equal-sibling 2-fan 1 2 MultiQC CheckQC Rundirparser run_folder__exit_right_0 (right) sink__entry_left_1 (left) col 0|1 row 0 grid created with nf-metro v1.1.0+dev

PR

Internal-source equal-sibling 2-fan 1 2 MultiQC CheckQC Rundirparser run_folder__exit_right_0 (right) sink__entry_left_1 (left) col 0|1 row 0 grid created with nf-metro v1.1.0+dev

Port Fed Three Branch Diamond changed

Base (main)

Port-fed Three-branch Diamond 1 2 Alpha Beta Gamma Prepare Join source__exit_right_0 (right) work__entry_left_1 (left) col 0|1 row 0 grid Alpha branch Beta branch Gamma branch created with nf-metro v1.1.0+dev

PR

Port-fed Three-branch Diamond 1 2 Alpha Beta Gamma Prepare Join source__exit_right_0 (right) work__entry_left_1 (left) col 0|1 row 0 grid Alpha branch Beta branch Gamma branch created with nf-metro v1.1.0+dev

Ported Symmetric Fan Centreline Trunk changed

Base (main)

Ported Symmetric Fan Centreline Trunk 1 2 3 Fetch Identify Report Source A Source B Source C Source D Source E Source F Merge input__exit_right_0 (right) fetch__exit_right_1 (right) fetch__entry_left_2 (left) report__entry_left_3 (left) col 0|1 col 1|2 row 0 grid Main created with nf-metro v1.1.0+dev

PR

Ported Symmetric Fan Centreline Trunk 1 2 3 Fetch Identify Report Source A Source B Source C Source D Source E Source F Merge input__exit_right_0 (right) fetch__exit_right_1 (right) fetch__entry_left_2 (left) report__entry_left_3 (left) col 0|1 col 1|2 row 0 grid Main created with nf-metro v1.1.0+dev

Symmetric Deadend Fanout changed

Base (main)

Symmetric Deadend Fanout 1 2 BW Coverage Split Entry Salmon Genomecov src__exit_right_0 (right) s1__entry_left_1 (left) col 0|1 row 0 grid Line A created with nf-metro v1.1.0+dev

PR

Symmetric Deadend Fanout 1 2 BW Coverage Split Entry Salmon Genomecov src__exit_right_0 (right) s1__entry_left_1 (left) col 0|1 row 0 grid Line A created with nf-metro v1.1.0+dev

Terminal Symmetric Fan changed

Base (main)

Terminal Fan 1 2 Input Shiny MultiQC Quarto Process source__exit_right_0 (right) reporting__entry_left_1 (left) col 0|1 row 0 grid A B created with nf-metro v1.1.0+dev

PR

Terminal Fan 1 2 Input Shiny MultiQC Quarto Process source__exit_right_0 (right) reporting__entry_left_1 (left) col 0|1 row 0 grid A B created with nf-metro v1.1.0+dev

Trunk Through Fan changed

Base (main)

Trunk Through Fan 1 2 3 Input Split Report Prepare Path Up Path Down Join source__exit_right_0 (right) middle__exit_right_1 (right) middle__entry_left_2 (left) sink__entry_left_3 (left) col 0|1 col 1|2 row 0 grid A B created with nf-metro v1.1.0+dev

PR

Trunk Through Fan 1 2 3 Input Split Report Prepare Path Up Path Down Join source__exit_right_0 (right) middle__exit_right_1 (right) middle__entry_left_2 (left) sink__entry_left_3 (left) col 0|1 col 1|2 row 0 grid A B created with nf-metro v1.1.0+dev

Serpentine Layout

Fold Fan Across changed

Base (main)

Proteomics Quantification Pipeline 1 2 3 4 5 6 7 Input Label Input Merge Aggregate Align Window Validate Fractionate Calculate Diff. Expression MultiQC Quantify Extract Extract Pool Apply Pathway Report Normalize Quantify Tag Quantify Volcano Plot Filter A Check Filter B Merge QC Filter Final QC sample_prep__exit_right_0 (right) tmt_quant__exit_right_1 (right) lfq_quant__exit_right_2 (right) dia_quant__exit_right_3 (right) normalize__exit_bottom_4 (bottom) stat_analysis__exit_left_5 (left) tmt_quant__entry_left_6 (left) lfq_quant__entry_left_7 (left) dia_quant__entry_left_8 (left) normalize__entry_left_9 (left) stat_analysis__entry_top_10 (top) reporting__entry_right_11 (right) __junction_12 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 3 grid TMT Labeling Label-Free DIA created with nf-metro v1.1.0+dev

PR

Proteomics Quantification Pipeline 1 2 3 4 5 6 7 Input Label Input Merge Aggregate Align Window Validate Fractionate Calculate Diff. Expression MultiQC Quantify Extract Extract Pool Apply Pathway Report Normalize Quantify Tag Quantify Volcano Plot Filter A Check Filter B Merge QC Filter Final QC sample_prep__exit_right_0 (right) tmt_quant__exit_right_1 (right) lfq_quant__exit_right_2 (right) dia_quant__exit_right_3 (right) normalize__exit_bottom_4 (bottom) stat_analysis__exit_left_5 (left) tmt_quant__entry_left_6 (left) lfq_quant__entry_left_7 (left) dia_quant__entry_left_8 (left) normalize__entry_left_9 (left) stat_analysis__entry_top_10 (top) reporting__entry_right_11 (right) __junction_12 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 2|3 row 0 grid row 1 grid row 2 grid row 0 grid row 3 grid row 3 grid TMT Labeling Label-Free DIA created with nf-metro v1.1.0+dev

Fold Stacked Branch changed

Base (main)

Single-Cell Multi-Omics Pipeline 1 2 3 4 5 6 7 8 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 2 3 4 5 6 7 8 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

Opposing Bypass Corridor changed

Base (main)

Opposing Bypass Corridor 1 2 3 4 6 7 8 5 Trim Align Quantify Report Call ORFs P-sites TE Assemble Transcripts preprocessing__exit_right_0 (right) alignment__exit_right_1 (right) quantification__exit_right_2 (right) orf_calling__exit_left_3 (left) psite_id__exit_left_4 (left) novel_transcripts__exit_left_5 (left) alignment__entry_left_6 (left) quantification__entry_left_7 (left) reporting__entry_left_8 (left) orf_calling__entry_top_9 (top) psite_id__entry_top_10 (top) te__entry_right_11 (right) novel_transcripts__entry_top_12 (top) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid row 1 grid Ribo-seq RNA-seq created with nf-metro v1.1.0+dev

PR

Opposing Bypass Corridor 1 2 3 4 6 7 8 5 Trim Align Quantify Report Call ORFs P-sites TE Assemble Transcripts preprocessing__exit_right_0 (right) alignment__exit_right_1 (right) quantification__exit_right_2 (right) orf_calling__exit_left_3 (left) psite_id__exit_left_4 (left) novel_transcripts__exit_left_5 (left) alignment__entry_left_6 (left) quantification__entry_left_7 (left) reporting__entry_left_8 (left) orf_calling__entry_top_9 (top) psite_id__entry_top_10 (top) te__entry_right_11 (right) novel_transcripts__entry_top_12 (top) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 0 grid row 0 grid row 0 grid row 0 grid row 1 grid row 1 grid row 1 grid row 1 grid Ribo-seq RNA-seq created with nf-metro v1.1.0+dev

Packed Cell Right Exit Left Entry Wrap changed

Base (main)

nf-core/genomeassembler 1 2 3 4 5 6 7 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 2 3 4 5 6 7 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

Packed Multiline Serpentine Grid changed

Base (main)

Packed multi-row grid 1 2 5 6 7 3 8 4 DATA DATA DATA DATA DATA DATA DATA D1 D3 G1 B1 D5 E2 F3 H1 G2 C1 D6 E1 F1 D7 D2 G3 G4 A1 B2 E3 G5 C2 G6 F2 G7 D4 E4 G8 A2 E5 G9 C3 A3 D8 A4 A5 A6 A7 A8 A9 A10 A11 A12 sec_d__exit_right_0 (right) sec_a__exit_right_1 (right) sec_b__exit_right_2 (right) sec_c__exit_right_3 (right) sec_e__exit_right_4 (right) sec_f__exit_right_5 (right) sec_e__entry_left_6 (left) sec_b__entry_left_7 (left) sec_c__entry_top_8 (top) sec_d__entry_left_9 (left) sec_f__entry_left_10 (left) sec_g__entry_left_11 (left) sec_h__entry_left_12 (left) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid __converge_file6_1 Line 1 Line 2 Line 3 created with nf-metro v1.1.0+dev

PR

Packed multi-row grid 1 2 5 6 7 3 8 4 DATA DATA DATA DATA DATA DATA DATA D1 D3 G1 B1 D5 E2 F3 H1 G2 C1 D6 E1 F1 D7 D2 G3 G4 A1 B2 E3 G5 C2 G6 F2 G7 D4 E4 G8 A2 E5 G9 C3 A3 D8 A4 A5 A6 A7 A8 A9 A10 A11 A12 sec_d__exit_right_0 (right) sec_a__exit_right_1 (right) sec_b__exit_right_2 (right) sec_c__exit_right_3 (right) sec_e__exit_right_4 (right) sec_f__exit_right_5 (right) sec_e__entry_left_6 (left) sec_b__entry_left_7 (left) sec_c__entry_top_8 (top) sec_d__entry_left_9 (left) sec_f__entry_left_10 (left) sec_g__entry_left_11 (left) sec_h__entry_left_12 (left) __junction_13 (?) __junction_14 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid __converge_file6_1 Line 1 Line 2 Line 3 created with nf-metro v1.1.0+dev

Reconverge Reversed Fold changed

Base (main)

Reconvergence Reversed Alt 1 2 3 4 5 6 7 8 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 2 3 4 5 6 7 8 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

Test Fixtures

Genomeassembly Organellar changed

Base (main)

sanger-tol/genomeassembly 1 2 4 5 6 3 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 2 4 5 6 3 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

Target Entry Runway Bypass changed

Base (main)

1 2 3 4 5 6 8 7 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 2 3 4 5 6 8 7 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

Tb Exit Terminal On Carrier changed

Base (main)

riboseq (te + psite_id excerpt) 1 2 4 3 5 BED ORF catalogue HTML riboWaltz HTML TE report Ribo-TISH plastid P-site Plastid P-site counts riboWaltz UMI-tools Dedup Salmon Merge ORF catalogue plastid Wiggle Prep TE counts Quantify ORF P-sites anota2seq DESeq2 deltaTE orf_calling__exit_right_0 (right) alignment__exit_right_1 (right) psite_id__exit_bottom_2 (bottom) quantification__exit_right_3 (right) psite_id__entry_left_4 (left) orf_calling__entry_left_5 (left) quantification__entry_left_6 (left) te__entry_left_7 (left) __junction_8 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 0 grid row 0 grid row 1 grid row 2 grid __converge_report_te_1 Ribo-seq Matched RNA-seq (optional) created with nf-metro v1.1.0+dev

PR

riboseq (te + psite_id excerpt) 1 2 4 3 5 BED ORF catalogue HTML riboWaltz HTML TE report Ribo-TISH plastid P-site Plastid P-site counts riboWaltz UMI-tools Dedup Salmon Merge ORF catalogue plastid Wiggle Prep TE counts Quantify ORF P-sites anota2seq DESeq2 deltaTE orf_calling__exit_right_0 (right) alignment__exit_right_1 (right) psite_id__exit_bottom_2 (bottom) quantification__exit_right_3 (right) psite_id__entry_left_4 (left) orf_calling__entry_left_5 (left) quantification__entry_left_6 (left) te__entry_left_7 (left) __junction_8 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 0 grid row 0 grid row 1 grid row 2 grid __converge_report_te_1 Ribo-seq Matched RNA-seq (optional) created with nf-metro v1.1.0+dev

Nextflow Conversions

Nf Variant Calling Tuned changed

Base (main)

Variant Calling Pipeline 1 2 3 4 BWA Index GATK HaplotypeCaller DeepVariant FastQC MultiQC FastP BWA-MEM BCFtools Stats SAMtools Sort SAMtools Index preprocess__exit_right_0 (right) alignment__exit_right_1 (right) variant_calling__exit_right_2 (right) alignment__entry_left_3 (left) variant_calling__entry_left_4 (left) reporting__entry_left_5 (left) __junction_6 (?) col 0|1 col 1|2 col 2|3 row 0 grid Main QC Reporting created with nf-metro v1.1.0+dev

PR

Variant Calling Pipeline 1 2 3 4 BWA Index GATK HaplotypeCaller DeepVariant FastQC MultiQC FastP BWA-MEM BCFtools Stats SAMtools Sort SAMtools Index preprocess__exit_right_0 (right) alignment__exit_right_1 (right) variant_calling__exit_right_2 (right) alignment__entry_left_3 (left) variant_calling__entry_left_4 (left) reporting__entry_left_5 (left) __junction_6 (?) col 0|1 col 1|2 col 2|3 row 0 grid Main QC Reporting created with nf-metro v1.1.0+dev

Nf Variant Calling Tuned Icons changed

Base (main)

Variant Calling Pipeline 1 2 3 4 FASTQ FASTA VCF HTML GATK HaplotypeCaller DeepVariant MultiQC BWA Index FastP BCFtools Stats FastQC BWA-MEM SAMtools Sort SAMtools Index preprocess__exit_right_0 (right) alignment__exit_right_1 (right) variant_calling__exit_right_2 (right) alignment__entry_left_3 (left) variant_calling__entry_left_4 (left) reporting__entry_left_5 (left) __junction_6 (?) col 0|1 col 1|2 col 2|3 row 0 grid Main QC Reporting created with nf-metro v1.1.0+dev

PR

Variant Calling Pipeline 1 2 3 4 FASTQ FASTA VCF HTML GATK HaplotypeCaller DeepVariant MultiQC BWA Index FastP BCFtools Stats FastQC BWA-MEM SAMtools Sort SAMtools Index preprocess__exit_right_0 (right) alignment__exit_right_1 (right) variant_calling__exit_right_2 (right) alignment__entry_left_3 (left) variant_calling__entry_left_4 (left) reporting__entry_left_5 (left) __junction_6 (?) col 0|1 col 1|2 col 2|3 row 0 grid Main QC Reporting created with nf-metro v1.1.0+dev

Off-track & Rails

Off Track Input Above Consumer changed

Base (main)

Long-read Methylation & Variant Atlas 1 2 3 4 5 6 7 8 FASTA Reference GTF Annotation BAM Aligned BED CpG islands bigWig Methylation POD5 modkit Clair3 Collect Aggregate IsoQuant JAFFAL Basecall minimap2 Pileup Phase VEP MultiQC Count Annotate Demux Sort DMR Filter Classify Report Normalize ReadQC Index intake__exit_right_0 (right) align__exit_right_1 (right) methcall__exit_right_2 (right) variants__exit_right_3 (right) expr__exit_right_4 (right) fusion__exit_right_5 (right) merge__exit_right_6 (right) align__entry_left_7 (left) methcall__entry_left_8 (left) variants__entry_left_9 (left) expr__entry_left_10 (left) fusion__entry_left_11 (left) report__entry_left_12 (left) merge__entry_left_13 (left) __junction_14 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 1|2 row 2|3 row 0 grid row 1 grid row 2 grid row 3 grid DNA variants RNA expression QC stream created with nf-metro v1.1.0+dev

PR

Long-read Methylation & Variant Atlas 1 2 3 4 5 6 7 8 FASTA Reference GTF Annotation BAM Aligned BED CpG islands bigWig Methylation POD5 modkit Clair3 Collect Aggregate IsoQuant JAFFAL Basecall minimap2 Pileup Phase VEP MultiQC Count Annotate Demux Sort DMR Filter Classify Report Normalize ReadQC Index intake__exit_right_0 (right) align__exit_right_1 (right) methcall__exit_right_2 (right) variants__exit_right_3 (right) expr__exit_right_4 (right) fusion__exit_right_5 (right) merge__exit_right_6 (right) align__entry_left_7 (left) methcall__entry_left_8 (left) variants__entry_left_9 (left) expr__entry_left_10 (left) fusion__entry_left_11 (left) report__entry_left_12 (left) merge__entry_left_13 (left) __junction_14 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0|1 row 1|2 row 2|3 row 0 grid row 1 grid row 2 grid row 3 grid DNA variants RNA expression QC stream created with nf-metro v1.1.0+dev

nf-core Pipelines

Pipeline Genomeassembly changed

Base (main)

sanger-tol/genomeassembly 1 2 3 4 5 FASTX CRAM FASTQ bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO Hifiasm 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) __junction_8 (?) __junction_9 (?) __junction_10 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

PR

sanger-tol/genomeassembly 1 2 3 4 5 FASTX CRAM FASTQ bwa-mem2 minimap2 asmstats minimap2 GFAStats purge_dups Longranger YaHS BUSCO Hifiasm 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) __junction_8 (?) __junction_9 (?) __junction_10 (?) __merge_3 (?) __merge_4 (?) __merge_5 (?) col 0|1 col 1|2 col 2|3 col 3|4 row 0 grid Assembly Long reads Hi-C reads 10X reads created with nf-metro v1.1.0+dev

Pipeline Variantbenchmarking changed

Base (main)

nf-core/variantbenchmarking 1 2 3 4 6 7 8 5 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 2 3 4 6 7 8 5 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

Pipeline Variantprioritization changed

Base (main)

nf-core/variantprioritization 1 2 3 5 4 VCF CNA HTML HTML Reformat VCF PCGR CPSR PCGR DB VEP Cache Intersect VCF tabix Reformat CNA bcftools/norm Prepare VCF bcftools/filter get_reference__exit_right_0 (right) preprocessing__exit_right_1 (right) format_files__exit_right_2 (right) run_cpsr__entry_left_3 (left) format_files__entry_left_4 (left) run_pcgr__entry_left_5 (left) __junction_6 (?) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid Somatic Germline Reference created with nf-metro v1.1.0+dev

PR

nf-core/variantprioritization 1 2 3 5 4 VCF CNA HTML HTML Reformat VCF PCGR CPSR PCGR DB VEP Cache Intersect VCF tabix Reformat CNA bcftools/norm Prepare VCF bcftools/filter get_reference__exit_right_0 (right) preprocessing__exit_right_1 (right) format_files__exit_right_2 (right) run_cpsr__entry_left_3 (left) format_files__entry_left_4 (left) run_pcgr__entry_left_5 (left) __junction_6 (?) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid Somatic Germline Reference created with nf-metro v1.1.0+dev

TB / BT Sections

Right Entry Over Top Tall Upstream changed

Base (main)

Over-top right entry, tall upstream 1 2 3 4 Prepare A Step 1 Prep C Merge Prepare B Step 2 Prep D Report Step 3 Step 4 Step 5 source__exit_right_0 (right) feeder__exit_right_1 (right) tall__entry_left_2 (left) target__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid Alpha Beta created with nf-metro v1.1.0+dev

PR

Over-top right entry, tall upstream 1 2 3 4 Prepare A Step 1 Prep C Merge Prepare B Step 2 Prep D Report Step 3 Step 4 Step 5 source__exit_right_0 (right) feeder__exit_right_1 (right) tall__entry_left_2 (left) target__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid row 1 grid Alpha Beta created with nf-metro v1.1.0+dev

Tb Internal Diagonal changed

Base (main)

TB Internal Diagonal 1 2 Start Demux Lane A End Lane B source__exit_right_0 (right) work__entry_top_1 (top) col 0|1 row 0 grid row 0 grid A B created with nf-metro v1.1.0+dev

PR

TB Internal Diagonal 1 2 Start Demux Lane A End Lane B source__exit_right_0 (right) work__entry_top_1 (top) col 0|1 row 0 grid row 0 grid A B created with nf-metro v1.1.0+dev

Tb Lr Exit Left changed

Base (main)

TB Left Exit 1 2 3 Start Process Publish End Collect prep__exit_right_0 (right) work__exit_left_1 (left) work__entry_top_2 (top) report__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid A B created with nf-metro v1.1.0+dev

PR

TB Left Exit 1 2 3 Start Process Publish End Collect prep__exit_right_0 (right) work__exit_left_1 (left) work__entry_top_2 (top) report__entry_right_3 (right) col 0|1 row 0|1 row 0 grid row 0 grid row 1 grid A B created with nf-metro v1.1.0+dev

Tb Lr Exit Right changed

Base (main)

TB Right Exit 1 2 3 Start Process Publish End Collect prep__exit_right_0 (right) work__exit_right_1 (right) work__entry_top_2 (top) report__entry_left_3 (left) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid A B created with nf-metro v1.1.0+dev

PR

TB Right Exit 1 2 3 Start Process Publish End Collect prep__exit_right_0 (right) work__exit_right_1 (right) work__entry_top_2 (top) report__entry_left_3 (left) col 0|1 col 1|2 row 0 grid row 0 grid row 0 grid A B created with nf-metro v1.1.0+dev

Basic Topologies

Self Crossing Bridge changed

Base (main)

Self-Crossing Bridge 1 3 4 2 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 3 4 2 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