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:
Intended improvements in the PR column
Unintended regressions (overlapping lines, shifted labels,
broken routing) in diagrams you did not mean to change
New renders (green added badge) or removed renders
(red removed badge)
Layout-quality metrics
Advisory only — nothing gates on these. green improved, red regressed. Lower is better except in the ↑ column.
03B Fan In Merge changed
Side by side Base only PR only
Base (main)
Fan-In Merge
1
Source
2
Step A
3
Step B
4
Sink
Produce
Produce
Process A
Process A
Process B
Process B
Collect
Collect
Prepare
Prepare
Refine A
Refine A
Refine B
Refine B
Report
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
Source
2
Step A
3
Step B
4
Sink
Produce
Produce
Process A
Process A
Process B
Process B
Collect
Collect
Prepare
Prepare
Refine A
Refine A
Refine B
Refine B
Report
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
Side by side Base only PR only
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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
Side by side Base only PR only
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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 Fan In Outer Slot changed
Side by side Base only PR only
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
Samplesheet
Fastp
Fastp
BWA-MEM
BWA-MEM
MOFA Factor Model
MOFA Factor Model
Salmon
Salmon
MACS2
MACS2
Dispatch
Dispatch
Demultiplex
Demultiplex
Contam Screen
Contam Screen
MarkDup
MarkDup
MultiQC Report
MultiQC Report
Tximport
Tximport
Annotate Peaks
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
Samplesheet
Fastp
Fastp
BWA-MEM
BWA-MEM
MOFA Factor Model
MOFA Factor Model
Salmon
Salmon
MACS2
MACS2
Dispatch
Dispatch
Demultiplex
Demultiplex
Contam Screen
Contam Screen
MarkDup
MarkDup
MultiQC Report
MultiQC Report
Tximport
Tximport
Annotate Peaks
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
Side by side Base only PR only
Base (main)
Seven-line leftward bypass far-side entry
1
Source
3
Middle
2
Target
Start
Start
Mid
Mid
Process
Process
Out
Out
MidOut
MidOut
End
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
Start
Mid
Mid
Process
Process
Out
Out
MidOut
MidOut
End
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
Side by side Base only PR only
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
Sniffles
WhatsHap Phase
WhatsHap Phase
CuteSV
CuteSV
Clair3
Clair3
ont-spectre CNVCaller
ont-spectre CNVCaller
LongTR
LongTR
Jasmine merge samples
Jasmine merge samples
VEP
VEP
Geneyx
Geneyx
Deepvariant
Deepvariant
Straglr
Straglr
GLNexus
GLNexus
SnpEff
SnpEff
SV Report
SV Report
TRGT
TRGT
AnnotSV
AnnotSV
samtools merge
samtools merge
cat FASTQ
cat FASTQ
WhatsHap Haplotag
WhatsHap Haplotag
Jasmine merge callers
Jasmine merge callers
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Sniffles
WhatsHap Phase
WhatsHap Phase
CuteSV
CuteSV
Clair3
Clair3
ont-spectre CNVCaller
ont-spectre CNVCaller
LongTR
LongTR
Jasmine merge samples
Jasmine merge samples
VEP
VEP
Geneyx
Geneyx
Deepvariant
Deepvariant
Straglr
Straglr
GLNexus
GLNexus
SnpEff
SnpEff
SV Report
SV Report
TRGT
TRGT
AnnotSV
AnnotSV
samtools merge
samtools merge
cat FASTQ
cat FASTQ
WhatsHap Haplotag
WhatsHap Haplotag
Jasmine merge callers
Jasmine merge callers
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Side by side Base only PR only
Base (main)
Disjoint Same-Line Bypass Trunks
1
Ingest
2
QC
3
Align
4
Call
5
Report
Input
Input
QC Step
QC Step
Align
Align
Call
Call
Report
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
Input
QC Step
QC Step
Align
Align
Call
Call
Report
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
Side by side Base only PR only
Base (main)
Dogleg Off Exempt Trunks - Distinct Line Regime
3
Left Target
2
Right Source
4
Bottom Sink
1
Skip Source
Collect
Collect
Input R
Input R
Collect B
Collect B
Step S
Step S
Output
Output
Hub R
Hub R
Output B
Output B
Out S
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
Collect
Input R
Input R
Collect B
Collect B
Step S
Step S
Output
Output
Hub R
Hub R
Output B
Output B
Out S
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
Side by side Base only PR only
Base (main)
Dogleg Off Exempt Trunks - Same Line Regime
2
Left Target
1
Right Source
3
New Target
Collect
Collect
Input R
Input R
Hub N
Hub N
Output
Output
Hub R
Hub R
Out N
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
Left Target
1
Right Source
3
New Target
Collect
Collect
Input R
Input R
Hub N
Hub N
Output
Output
Hub R
Hub R
Out N
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
Side by side Base only PR only
Base (main)
Fold Bypass Creep
1
Prep
2
Calling
3
Report
VCF
Caller A
Caller A
Caller B
Caller B
MultiQC
MultiQC
Align
Align
Stats
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
Prep
2
Calling
3
Report
VCF
Caller A
Caller A
Caller B
Caller B
MultiQC
MultiQC
Align
Align
Stats
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
Side by side Base only PR only
Base (main)
Fold Bypass Creep (tight)
1
Prep
2
Calling
3
Report
VCF
Caller A
Caller A
Caller B
Caller B
MultiQC
MultiQC
Align
Align
Stats
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
Prep
2
Calling
3
Report
VCF
Caller A
Caller A
Caller B
Caller B
MultiQC
MultiQC
Align
Align
Stats
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
Side by side Base only PR only
Base (main)
Same-line fan with distinct descent
1
Source
2
Continue
3
Far green
4
Near red
5
Mid red
Input
Input
Carry on
Carry on
FarStep
FarStep
NearStep
NearStep
MidStep
MidStep
Process
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
Source
2
Continue
3
Far green
4
Near red
5
Mid red
Input
Input
Carry on
Carry on
FarStep
FarStep
NearStep
NearStep
MidStep
MidStep
Process
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
Compact Gap Peer Conflict changed
Side by side Base only PR only
Base (main)
Compaction Gap Peer Conflict
1
Source
2
Process
3
Sink
Input
Input
Fork
Fork
End
End
Prepare
Prepare
Alpha Gamma
Alpha Gamma
Beta Node
Beta Node
Merge
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
Source
2
Process
3
Sink
Input
Input
Fork
Fork
End
End
Prepare
Prepare
Alpha Gamma
Alpha Gamma
Beta Node
Beta Node
Merge
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
Side by side Base only PR only
Base (main)
Exit run, three drop columns
1
A
2
B
3
C
4
D
5
E
Step A1
Step A1
Step B1
Step B1
Step C1
Step C1
Step E1
Step E1
Step D1
Step D1
Step A2
Step A2
Step B2
Step B2
Step C2
Step C2
Step E2
Step E2
Step D2
Step D2
Step B3
Step B3
Step C3
Step C3
Step B4
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 A1
Step B1
Step B1
Step C1
Step C1
Step E1
Step E1
Step D1
Step D1
Step A2
Step A2
Step B2
Step B2
Step C2
Step C2
Step E2
Step E2
Step D2
Step D2
Step B3
Step B3
Step C3
Step C3
Step B4
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
Side by side Base only PR only
Base (main)
Independent Exit Lane Frames
1
Feeder
2
Settling source
3
Side
4
Straight target
5
Lower target
12
Independent target
11
Independent source
6
Direct feeder
7
Direct source
8
Vertical direct target
9
Vertical side exit
10
Side report
13
Vertical source
14
Vertical target
Before
Before
Direct in
Direct in
Vertical A
Vertical A
Vertical C
Vertical C
Side in
Side in
Feed
Feed
Side
Side
Straight
Straight
Lower
Lower
Independent in
Independent in
Independent out
Independent out
Direct feed
Direct feed
Direct out
Direct out
Side result
Side result
Split
Split
Direct done
Direct done
Vertical B
Vertical B
Vertical D
Vertical D
Side out
Side out
Vertical E
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
Independent source
6
Direct feeder
7
Direct source
8
Vertical direct target
9
Vertical side exit
10
Side report
13
Vertical source
14
Vertical target
Before
Before
Direct in
Direct in
Vertical A
Vertical A
Vertical C
Vertical C
Side in
Side in
Feed
Feed
Side
Side
Straight
Straight
Lower
Lower
Independent in
Independent in
Independent out
Independent out
Direct feed
Direct feed
Direct out
Direct out
Side result
Side result
Split
Split
Direct done
Direct done
Vertical B
Vertical B
Vertical D
Vertical D
Side out
Side out
Vertical E
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
Side by side Base only PR only
Base (main)
Complex Multipath
1
Input
2
Fast Track
3
Full Pre-process
5
Standard Analysis
4
Deep Analysis
6
Output
Raw Data
Raw Data
Quick Align
Quick Align
Aggregate
Aggregate
Trim
Trim
Align
Align
HQ Align
HQ Align
Validate
Validate
Quick Quant
Quick Quant
Report
Report
Filter
Filter
Quantify
Quantify
Dedup
Dedup
QC Check
QC Check
HQ Quantify
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
Raw Data
Quick Align
Quick Align
Aggregate
Aggregate
Trim
Trim
Align
Align
HQ Align
HQ Align
Validate
Validate
Quick Quant
Quick Quant
Report
Report
Filter
Filter
Quantify
Quantify
Dedup
Dedup
QC Check
QC Check
HQ Quantify
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
Convergence Stacked Sink changed
Side by side Base only PR only
Base (main)
Convergence Stacked Sink
1
Prep
4
Aux Input
2
Align
5
Repeats
3
Dedup
6
Merge
7
Report
Input
Input
Load
Load
Map
Map
Detect
Detect
Mark
Mark
Combine
Combine
Summarise
Summarise
Output
Output
Index
Index
Sort
Sort
Genotype
Genotype
Recal
Recal
Refine
Refine
Publish
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
Prep
4
Aux Input
2
Align
5
Repeats
3
Dedup
6
Merge
7
Report
Input
Input
Load
Load
Map
Map
Detect
Detect
Mark
Mark
Combine
Combine
Summarise
Summarise
Output
Output
Index
Index
Sort
Sort
Genotype
Genotype
Recal
Recal
Refine
Refine
Publish
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
Side by side Base only PR only
Base (main)
Fan-in to a distant terminus
1
Translational efficiency
HTML
Report
Prep
Prep
anota2seq
anota2seq
deltaTE
deltaTE
DOTSeq
DOTSeq
ORFquant
ORFquant
ORFtest
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
Translational efficiency
HTML
Report
Prep
Prep
anota2seq
anota2seq
deltaTE
deltaTE
DOTSeq
DOTSeq
ORFquant
ORFquant
ORFtest
ORFtest
row 0 grid
__converge_report_1
__converge_report_2
Line A
created with nf-metro v1.1.0+dev
Merge Adjacent Feeder changed
Side by side Base only PR only
Base (main)
Merge Adjacent Feeder
1
Source
2
Middle
3
Sink
4
Report
Score
Score
Produce
Produce
Collect
Collect
Summarise
Summarise
Plot
Plot
Filter
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
Source
2
Middle
3
Sink
4
Report
Score
Score
Produce
Produce
Collect
Collect
Summarise
Summarise
Plot
Plot
Filter
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
Side by side Base only PR only
Base (main)
Merge Around Below Leftmost
1
Source 1
2
Source 2
3
Extra
4
Target
Step A
Step A
Step B
Step B
Extra Step
Extra Step
Combine
Combine
Out A
Out A
Out B
Out B
Extra Out
Extra Out
Result
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
Source 1
2
Source 2
3
Extra
4
Target
Step A
Step A
Step B
Step B
Extra Step
Extra Step
Combine
Combine
Out A
Out A
Out B
Out B
Extra Out
Extra Out
Result
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
Side by side Base only PR only
Base (main)
Bottommost-Row Merge Inter-Row Bypass
1
Fan Source A
2
Fan Source B
3
Side
5
Middle
4
Target
In
In
In
In
Side
Side
Process
Process
Process
Process
Out
Out
Out
Out
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 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
In
In
Side
Side
Process
Process
Process
Process
Out
Out
Out
Out
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 0 grid
row 1 grid
row 2 grid
A
B
created with nf-metro v1.1.0+dev
Merge Feeder Shared Channel Gap changed
Side by side Base only PR only
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
In
In
Side
Side
Process
Process
LM
LM
Process
Process
Out
Out
Out
Out
Out
Out
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
In
In
Side
Side
Process
Process
LM
LM
Process
Process
Out
Out
Out
Out
Out
Out
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
Side by side Base only PR only
Base (main)
Report feeders from three columns
1
A
2
B
3
C
4
D
5
E
Step A1
Step A1
Step B1
Step B1
Step C1
Step C1
Step E1
Step E1
Step D1
Step D1
Step A2
Step A2
Step B2
Step B2
Step C2
Step C2
Step E2
Step E2
Step D2
Step D2
Step B3
Step B3
Step C3
Step C3
Step B4
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
A
2
B
3
C
4
D
5
E
Step A1
Step A1
Step B1
Step B1
Step C1
Step C1
Step E1
Step E1
Step D1
Step D1
Step A2
Step A2
Step B2
Step B2
Step C2
Step C2
Step E2
Step E2
Step D2
Step D2
Step B3
Step B3
Step C3
Step C3
Step B4
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
Side by side Base only PR only
Base (main)
Merge Leftmost Sink Branch
1
Blocker
2
Step A
3
Step B
4
Extra
5
Sink
Block Start
Block Start
Process A
Process A
Process B
Process B
Extra
Extra
Collect
Collect
Block End
Block End
Out A
Out A
Out B
Out B
Extra Out
Extra Out
Report
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
Blocker
2
Step A
3
Step B
4
Extra
5
Sink
Block Start
Block Start
Process A
Process A
Process B
Process B
Extra
Extra
Collect
Collect
Block End
Block End
Out A
Out A
Out B
Out B
Extra Out
Extra Out
Report
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
Side by side Base only PR only
Base (main)
Merge trunk pull-away cross-row sibling
1
Wide Source
2
Obstacle
3
Sibling
4
Side Dest
5
Target
Start
Start
Block
Block
Step
Step
Side
Side
Merge
Merge
Out
Out
Pass
Pass
Done
Done
Out
Out
Report
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
Wide Source
2
Obstacle
3
Sibling
4
Side Dest
5
Target
Start
Start
Block
Block
Step
Step
Side
Side
Merge
Merge
Out
Out
Pass
Pass
Done
Done
Out
Out
Report
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
Side by side Base only PR only
Base (main)
Merge Right Entry Cross Row
4
Sink
1
Source
2
Extra
3
Step A
Collect
Collect
Produce
Produce
Extra
Extra
Process A
Process A
Report
Report
Prepare
Prepare
Extra Out
Extra Out
Out A
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
Collect
Produce
Produce
Extra
Extra
Process A
Process A
Report
Report
Prepare
Prepare
Extra Out
Extra Out
Out A
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
Side by side Base only PR only
Base (main)
Merge Trunk Out-of-Range Section
1
Source Far
2
Mid
3
Source Near
4
Sink
5
Extra
6
Other Row
Merge
Merge
Far
Far
Mid Step
Mid Step
Near
Near
Extra Step
Extra Step
Other
Other
Report
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
Source Far
2
Mid
3
Source Near
4
Sink
5
Extra
6
Other Row
Merge
Merge
Far
Far
Mid Step
Mid Step
Near
Near
Extra Step
Extra Step
Other
Other
Report
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
Side by side Base only PR only
Base (main)
Merge Trunk Over Low Section
1
Ingest
2
Tall
3
Proc 2
4
Collect
5
Sub
Read
Read
Branch
Branch
Gather
Gather
Aux
Aux
Step
Step
Path A
Path A
Split
Split
Path B
Path B
Report
Report
Done
Done
Path C
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
Ingest
2
Tall
3
Proc 2
4
Collect
5
Sub
Read
Read
Branch
Branch
Gather
Gather
Aux
Aux
Step
Step
Path A
Path A
Split
Split
Path B
Path B
Report
Report
Done
Done
Path C
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
Cross Row Gap Wrap changed
Side by side Base only PR only
Base (main)
Cross-Row Gap Wrap
1
Ingest
2
Align
3
Dedup
4
Merge
5
Report
Read
Read
Map
Map
Mark
Mark
Combine
Combine
Summarise
Summarise
QC
QC
Sort
Sort
Recal
Recal
Refine
Refine
Publish
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
Ingest
2
Align
3
Dedup
4
Merge
5
Report
Read
Read
Map
Map
Mark
Mark
Combine
Combine
Summarise
Summarise
QC
QC
Sort
Sort
Recal
Recal
Refine
Refine
Publish
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
Side by side Base only PR only
Base (main)
Multi-carrier off-row exit climb
1
Pre-processing
2
Small variant calling
3
Depth & repeats
FASTQ
BAM
uBAM
Clair3
Clair3
LongTR
LongTR
Deepvariant
Deepvariant
ont-spectre
ont-spectre
samtools merge
samtools merge
cat FASTQ
cat FASTQ
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Pre-processing
2
Small variant calling
3
Depth & repeats
FASTQ
BAM
uBAM
Clair3
Clair3
LongTR
LongTR
Deepvariant
Deepvariant
ont-spectre
ont-spectre
samtools merge
samtools merge
cat FASTQ
cat FASTQ
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Side by side Base only PR only
Base (main)
Orbit - Perp Exit, Row Behind
1
Prepare
2
Process
3
Archive
Stage
Stage
Compute
Compute
Store
Store
Check
Check
Reduce
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
Prepare
2
Process
3
Archive
Stage
Stage
Compute
Compute
Store
Store
Check
Check
Reduce
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
Diagonal Labels changed
Side by side Base only PR only
Base (main)
Diagonal Labels (dense trunk)
1
Pre-processing
2
Variant calling
FASTQ
VCF
split by analysis
split by analysis
FastQC
FastQC
GATK
GATK
Mutect2
Mutect2
Strelka2
Strelka2
FastP
FastP
merge VCFs
merge VCFs
UMI consensus
UMI consensus
BWA-MEM
BWA-MEM
samtools merge/index
samtools merge/index
MarkDuplicates
MarkDuplicates
BaseRecalibrator
BaseRecalibrator
ApplyBQSR
ApplyBQSR
mosdepth
mosdepth
NGSCheckmate
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
Pre-processing
2
Variant calling
FASTQ
VCF
split by analysis
split by analysis
FastQC
FastQC
GATK
GATK
Mutect2
Mutect2
Strelka2
Strelka2
FastP
FastP
merge VCFs
merge VCFs
UMI consensus
UMI consensus
BWA-MEM
BWA-MEM
samtools merge/index
samtools merge/index
MarkDuplicates
MarkDuplicates
BaseRecalibrator
BaseRecalibrator
ApplyBQSR
ApplyBQSR
mosdepth
mosdepth
NGSCheckmate
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
Side by side Base only PR only
Base (main)
Multi-section cell packing
1
Preprocessing
2
GATK
4
Variant Calling
5
Normalize
3
Realignment
6
Reporting
7
Consensus
Input
Input
Call
Call
Pileup
Pileup
Norm
Norm
Index
Index
Report
Report
Consensus
Consensus
Trim
Trim
Filter
Filter
Genotype
Genotype
Annotate
Annotate
Realign
Realign
Summary
Summary
Final
Final
Phase
Phase
Dedup
Dedup
Recal
Recal
BQSR
BQSR
Score
Score
Merge
Merge
Emit
Emit
Sort
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
Preprocessing
2
GATK
4
Variant Calling
5
Normalize
3
Realignment
6
Reporting
7
Consensus
Input
Input
Call
Call
Pileup
Pileup
Norm
Norm
Index
Index
Report
Report
Consensus
Consensus
Trim
Trim
Filter
Filter
Genotype
Genotype
Annotate
Annotate
Realign
Realign
Summary
Summary
Final
Final
Phase
Phase
Dedup
Dedup
Recal
Recal
BQSR
BQSR
Score
Score
Merge
Merge
Emit
Emit
Sort
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
Side by side Base only PR only
Base (main)
Multi-row source, stacked fan
1
Alignment
2
QC
3
Quantification
4
Fusion detection
FASTQ
Reads
sambamba markdup
sambamba markdup
RSEM
RSEM
Arriba
Arriba
STAR-Fusion
STAR-Fusion
flagstat + mosdepth
flagstat + mosdepth
BBDuk trim
BBDuk trim
RNA-SeQC
RNA-SeQC
Gene annotation
Gene annotation
Merge fusions
Merge fusions
STAR 2-pass
STAR 2-pass
Draw fusions
Draw fusions
samtools CRAM
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
Alignment
2
QC
3
Quantification
4
Fusion detection
FASTQ
Reads
sambamba markdup
sambamba markdup
RSEM
RSEM
Arriba
Arriba
STAR-Fusion
STAR-Fusion
flagstat + mosdepth
flagstat + mosdepth
BBDuk trim
BBDuk trim
RNA-SeQC
RNA-SeQC
Gene annotation
Gene annotation
Merge fusions
Merge fusions
STAR 2-pass
STAR 2-pass
Draw fusions
Draw fusions
samtools CRAM
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
Side by side Base only PR only
Base (main)
Peel-off Straight Drop Near Wall
1
Preprocessing
2
Alignment
3
Quantification
4
TE
5
Novel Transcripts
Trim
Trim
Align
Align
Quantify
Quantify
TE
TE
Assemble
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
Preprocessing
2
Alignment
3
Quantification
4
TE
5
Novel Transcripts
Trim
Trim
Align
Align
Quantify
Quantify
TE
TE
Assemble
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
Side by side Base only PR only
Base (main)
Straight Drop Below
1
Top
2
Bottom
3
Sink
Source
Source
Assemble
Assemble
Collect
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
Top
2
Bottom
3
Sink
Source
Source
Assemble
Assemble
Collect
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
Side by side Base only PR only
Base (main)
Top Entry Fed From Left Neighbour
1
Intake
2
Screen
3
Producer
4
Consumer
Ref
Load
Load
Filter
Filter
Analyse
Analyse
Prep
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
Intake
2
Screen
3
Producer
4
Consumer
Ref
Load
Load
Filter
Filter
Analyse
Analyse
Prep
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
Differentialabundance changed
Side by side Base only PR only
Base (main)
1
Data import and preparation
2
Differential analysis
3
Functional enrichment
5
Reporting
4
Plots
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
shinyngs
Exploratory
Exploratory
limma
limma
Quarto report
Quarto report
Differential
Differential
DESeq2
DESeq2
dream
dream
propd
propd
gprofiler2
gprofiler2
grea
grea
GSEA
GSEA
Annotate results
Annotate results
Zip bundle
Zip bundle
decoupler
decoupler
GTF to table
GTF to table
affy load
affy load
proteus
proteus
GEOquery
GEOquery
Validate
Validate
Filter matrix
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
Data import and preparation
2
Differential analysis
3
Functional enrichment
5
Reporting
4
Plots
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
shinyngs
Exploratory
Exploratory
limma
limma
Quarto report
Quarto report
Differential
Differential
DESeq2
DESeq2
dream
dream
propd
propd
gprofiler2
gprofiler2
grea
grea
GSEA
GSEA
Annotate results
Annotate results
Zip bundle
Zip bundle
decoupler
decoupler
GTF to table
GTF to table
affy load
affy load
proteus
proteus
GEOquery
GEOquery
Validate
Validate
Filter matrix
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
Side by side Base only PR only
Base (main)
1
Data import and preparation
2
Differential analysis
3
Functional enrichment
5
Reporting
4
Plots
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
shinyngs
Exploratory
Exploratory
limma
limma
Quarto report
Quarto report
Differential
Differential
DESeq2
DESeq2
dream
dream
propd
propd
gprofiler2
gprofiler2
grea
grea
GSEA
GSEA
Annotate results
Annotate results
Zip bundle
Zip bundle
decoupler
decoupler
GTF to table
GTF to table
affy load
affy load
proteus
proteus
GEOquery
GEOquery
Validate
Validate
Filter matrix
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
Data import and preparation
2
Differential analysis
3
Functional enrichment
5
Reporting
4
Plots
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
shinyngs
Exploratory
Exploratory
limma
limma
Quarto report
Quarto report
Differential
Differential
DESeq2
DESeq2
dream
dream
propd
propd
gprofiler2
gprofiler2
grea
grea
GSEA
GSEA
Annotate results
Annotate results
Zip bundle
Zip bundle
decoupler
decoupler
GTF to table
GTF to table
affy load
affy load
proteus
proteus
GEOquery
GEOquery
Validate
Validate
Filter matrix
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
Side by side Base only PR only
Base (main)
sanger-tol/genomeassembly
1
Raw assembly
2
Purging
3
Polishing
4
Scaffolding
5
Genome QC
FASTX
CRAM
FASTQ
bwa-mem2
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
hifiasm
hifiasm
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
Raw assembly
2
Purging
3
Polishing
4
Scaffolding
5
Genome QC
FASTX
CRAM
FASTQ
bwa-mem2
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
hifiasm
hifiasm
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
Side by side Base only PR only
Base (main)
Variant Calling Pipeline
1
Pre-processing
2
Variant calling
3
Post-processing
4
Annotation
5
Reporting
FASTQ
BAM
CRAM
VCF
HTML
MultiQC
MultiQC
Filter VCFs
Filter VCFs
snpEff
snpEff
FastQC
FastQC
HaplotypeCaller
HaplotypeCaller
Normalize
Normalize
VEP
VEP
FastP
FastP
DeepVariant
DeepVariant
Sentieon DNAscope
Sentieon DNAscope
Sentieon Haplotyper
Sentieon Haplotyper
FreeBayes
FreeBayes
Strelka
Strelka
bcftools mpileup
bcftools mpileup
Manta
Manta
TIDDIT
TIDDIT
CNVkit
CNVkit
indexcov
indexcov
Mutect2
Mutect2
LoFreq
LoFreq
Sentieon TNscope
Sentieon TNscope
Control-FREEC
Control-FREEC
MSIsensor2
MSIsensor2
MuSE
MuSE
ASCAT
ASCAT
MSIsensor-pro
MSIsensor-pro
Concatenate
Concatenate
bcftools annotate
bcftools annotate
UMI consensus
UMI consensus
BWA-MEM
BWA-MEM
Consensus
Consensus
SnpSift
SnpSift
BWA-MEM2
BWA-MEM2
DragMap
DragMap
Sentieon BWA
Sentieon BWA
samtools merge/index
samtools merge/index
Varlociraptor
Varlociraptor
MarkDuplicates
MarkDuplicates
bcftools stats
bcftools stats
Sentieon Dedup
Sentieon Dedup
BaseRecalibrator
BaseRecalibrator
VCFtools
VCFtools
ApplyBQSR
ApplyBQSR
mosdepth
mosdepth
NGSCheckmate
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
Pre-processing
2
Variant calling
3
Post-processing
4
Annotation
5
Reporting
FASTQ
BAM
CRAM
VCF
HTML
MultiQC
MultiQC
Filter VCFs
Filter VCFs
snpEff
snpEff
FastQC
FastQC
HaplotypeCaller
HaplotypeCaller
Normalize
Normalize
VEP
VEP
FastP
FastP
DeepVariant
DeepVariant
Sentieon DNAscope
Sentieon DNAscope
Sentieon Haplotyper
Sentieon Haplotyper
FreeBayes
FreeBayes
Strelka
Strelka
bcftools mpileup
bcftools mpileup
Manta
Manta
TIDDIT
TIDDIT
CNVkit
CNVkit
indexcov
indexcov
Mutect2
Mutect2
LoFreq
LoFreq
Sentieon TNscope
Sentieon TNscope
Control-FREEC
Control-FREEC
MSIsensor2
MSIsensor2
MuSE
MuSE
ASCAT
ASCAT
MSIsensor-pro
MSIsensor-pro
Concatenate
Concatenate
bcftools annotate
bcftools annotate
UMI consensus
UMI consensus
BWA-MEM
BWA-MEM
Consensus
Consensus
SnpSift
SnpSift
BWA-MEM2
BWA-MEM2
DragMap
DragMap
Sentieon BWA
Sentieon BWA
samtools merge/index
samtools merge/index
Varlociraptor
Varlociraptor
MarkDuplicates
MarkDuplicates
bcftools stats
bcftools stats
Sentieon Dedup
Sentieon Dedup
BaseRecalibrator
BaseRecalibrator
VCFtools
VCFtools
ApplyBQSR
ApplyBQSR
mosdepth
mosdepth
NGSCheckmate
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
Side by side Base only PR only
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
Sniffles
WhatsHap Phase
WhatsHap Phase
CuteSV
CuteSV
Clair3
Clair3
ont-spectre CNVCaller
ont-spectre CNVCaller
LongTR
LongTR
Jasmine merge samples
Jasmine merge samples
VEP
VEP
Geneyx
Geneyx
Deepvariant
Deepvariant
Straglr
Straglr
GLNexus
GLNexus
SnpEff
SnpEff
SV Report
SV Report
TRGT
TRGT
AnnotSV
AnnotSV
samtools merge
samtools merge
cat FASTQ
cat FASTQ
WhatsHap Haplotag
WhatsHap Haplotag
Jasmine merge callers
Jasmine merge callers
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Sniffles
WhatsHap Phase
WhatsHap Phase
CuteSV
CuteSV
Clair3
Clair3
ont-spectre CNVCaller
ont-spectre CNVCaller
LongTR
LongTR
Jasmine merge samples
Jasmine merge samples
VEP
VEP
Geneyx
Geneyx
Deepvariant
Deepvariant
Straglr
Straglr
GLNexus
GLNexus
SnpEff
SnpEff
SV Report
SV Report
TRGT
TRGT
AnnotSV
AnnotSV
samtools merge
samtools merge
cat FASTQ
cat FASTQ
WhatsHap Haplotag
WhatsHap Haplotag
Jasmine merge callers
Jasmine merge callers
minimap2
minimap2
samtools sort/index
samtools sort/index
mosdepth
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
Side by side Base only PR only
Base (main)
Fan Branches with Additional Outputs
1
Input
2
Fetch orthologs
3
Reporting
Identify taxon
Identify taxon
Generate reports
Generate reports
OMA online
OMA online
OMA local
OMA local
PANTHER online
PANTHER online
PANTHER local
PANTHER local
OrthoInspector online
OrthoInspector online
EggNOG local
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
Input
2
Fetch orthologs
3
Reporting
Identify taxon
Identify taxon
Generate reports
Generate reports
OMA online
OMA online
OMA local
OMA local
PANTHER online
PANTHER online
PANTHER local
PANTHER local
OrthoInspector online
OrthoInspector online
EggNOG local
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
Side by side Base only PR only
Base (main)
nf-core/funcprofiler (upstream)
1
Input
2
Functional Profiling
3
Quality Check
4
Output
Short Reads
Short Reads
Input Databases
Input Databases
HUMAnN v3
HUMAnN v3
MultiQC
MultiQC
Results Directory
Results Directory
HUMAnN v4
HUMAnN v4
FMH FunProfiler
FMH FunProfiler
RGI
RGI
mifaser
mifaser
DIAMOND
DIAMOND
eggNOG-mapper
eggNOG-mapper
Preprocess
Preprocess
MERGE_RUNS
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
Short Reads
Input Databases
Input Databases
HUMAnN v3
HUMAnN v3
MultiQC
MultiQC
Results Directory
Results Directory
HUMAnN v4
HUMAnN v4
FMH FunProfiler
FMH FunProfiler
RGI
RGI
mifaser
mifaser
DIAMOND
DIAMOND
eggNOG-mapper
eggNOG-mapper
Preprocess
Preprocess
MERGE_RUNS
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
Side by side Base only PR only
Base (main)
Internal-source equal-sibling 2-fan
1
Run Folder
2
Aggregate
MultiQC
MultiQC
CheckQC
CheckQC
Rundirparser
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
Run Folder
2
Aggregate
MultiQC
MultiQC
CheckQC
CheckQC
Rundirparser
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
Side by side Base only PR only
Base (main)
Port-fed Three-branch Diamond
1
Source
2
Port-fed work
Alpha
Alpha
Beta
Beta
Gamma
Gamma
Prepare
Prepare
Join
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
Source
2
Port-fed work
Alpha
Alpha
Beta
Beta
Gamma
Gamma
Prepare
Prepare
Join
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
Side by side Base only PR only
Base (main)
Ported Symmetric Fan Centreline Trunk
1
Input
2
Fetch
3
Report
Fetch
Fetch
Identify
Identify
Report
Report
Source A
Source A
Source B
Source B
Source C
Source C
Source D
Source D
Source E
Source E
Source F
Source F
Merge
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
Input
2
Fetch
3
Report
Fetch
Fetch
Identify
Identify
Report
Report
Source A
Source A
Source B
Source B
Source C
Source C
Source D
Source D
Source E
Source E
Source F
Source F
Merge
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
Side by side Base only PR only
Base (main)
Symmetric Deadend Fanout
1
Src
2
S1
BW
Coverage
Split
Split
Entry
Entry
Salmon
Salmon
Genomecov
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
Src
2
S1
BW
Coverage
Split
Split
Entry
Entry
Salmon
Salmon
Genomecov
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
Side by side Base only PR only
Base (main)
Terminal Fan
1
Source
2
Reporting
Input
Input
Shiny
Shiny
MultiQC
MultiQC
Quarto
Quarto
Process
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
Source
2
Reporting
Input
Input
Shiny
Shiny
MultiQC
MultiQC
Quarto
Quarto
Process
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
Side by side Base only PR only
Base (main)
Trunk Through Fan
1
Source
2
Middle
3
Sink
Input
Input
Split
Split
Report
Report
Prepare
Prepare
Path Up
Path Up
Path Down
Path Down
Join
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
Source
2
Middle
3
Sink
Input
Input
Split
Split
Report
Report
Prepare
Prepare
Path Up
Path Up
Path Down
Path Down
Join
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
Fold Fan Across changed
Side by side Base only PR only
Base (main)
Proteomics Quantification Pipeline
1
Sample Preparation
2
TMT Quantification
3
Label-Free Quantification
4
DIA Quantification
5
Normalization
6
Statistical Analysis
7
Reporting
Input
Input
Label
Label
Input
Input
Merge
Merge
Aggregate
Aggregate
Align
Align
Window
Window
Validate
Validate
Fractionate
Fractionate
Calculate
Calculate
Diff. Expression
Diff. Expression
MultiQC
MultiQC
Quantify
Quantify
Extract
Extract
Extract
Extract
Pool
Pool
Apply
Apply
Pathway
Pathway
Report
Report
Normalize
Normalize
Quantify
Quantify
Tag
Tag
Quantify
Quantify
Volcano Plot
Volcano Plot
Filter A
Filter A
Check
Check
Filter B
Filter B
Merge
Merge
QC Filter
QC Filter
Final QC
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
Sample Preparation
2
TMT Quantification
3
Label-Free Quantification
4
DIA Quantification
5
Normalization
6
Statistical Analysis
7
Reporting
Input
Input
Label
Label
Input
Input
Merge
Merge
Aggregate
Aggregate
Align
Align
Window
Window
Validate
Validate
Fractionate
Fractionate
Calculate
Calculate
Diff. Expression
Diff. Expression
MultiQC
MultiQC
Quantify
Quantify
Extract
Extract
Extract
Extract
Pool
Pool
Apply
Apply
Pathway
Pathway
Report
Report
Normalize
Normalize
Quantify
Quantify
Tag
Tag
Quantify
Quantify
Volcano Plot
Volcano Plot
Filter A
Filter A
Check
Check
Filter B
Filter B
Merge
Merge
QC Filter
QC Filter
Final QC
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
Side by side Base only PR only
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
Input
Normalize
Normalize
Merge Modalities
Merge Modalities
Cell Typing
Cell Typing
Aggregate
Aggregate
Peak Calling
Peak Calling
Normalize
Normalize
Doublet Detection
Doublet Detection
Demux
Demux
Cluster
Cluster
WNN
WNN
Trajectory
Trajectory
Render Report
Render Report
Motif Analysis
Motif Analysis
Quantify
Quantify
Ambient RNA
Ambient RNA
Raw QC
Raw QC
Markers
Markers
UMAP
UMAP
Gene Reg. Network
Gene Reg. Network
Footprinting
Footprinting
Visualize
Visualize
QC Metrics
QC Metrics
Trim
Trim
Trajectories
Trajectories
Coverage
Coverage
Filter
Filter
DGE
DGE
Clean QC
Clean QC
Classify
Classify
Sort
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
Input
Normalize
Normalize
Merge Modalities
Merge Modalities
Cell Typing
Cell Typing
Aggregate
Aggregate
Peak Calling
Peak Calling
Normalize
Normalize
Doublet Detection
Doublet Detection
Demux
Demux
Cluster
Cluster
WNN
WNN
Trajectory
Trajectory
Render Report
Render Report
Motif Analysis
Motif Analysis
Quantify
Quantify
Ambient RNA
Ambient RNA
Raw QC
Raw QC
Markers
Markers
UMAP
UMAP
Gene Reg. Network
Gene Reg. Network
Footprinting
Footprinting
Visualize
Visualize
QC Metrics
QC Metrics
Trim
Trim
Trajectories
Trajectories
Coverage
Coverage
Filter
Filter
DGE
DGE
Clean QC
Clean QC
Classify
Classify
Sort
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
Side by side Base only PR only
Base (main)
Opposing Bypass Corridor
1
Preprocessing
2
Alignment
3
Quantification
4
Reporting
6
ORF Calling
7
P-site ID
8
TE
5
Novel Transcripts
Trim
Trim
Align
Align
Quantify
Quantify
Report
Report
Call ORFs
Call ORFs
P-sites
P-sites
TE
TE
Assemble Transcripts
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
Preprocessing
2
Alignment
3
Quantification
4
Reporting
6
ORF Calling
7
P-site ID
8
TE
5
Novel Transcripts
Trim
Trim
Align
Align
Quantify
Quantify
Report
Report
Call ORFs
Call ORFs
P-sites
P-sites
TE
TE
Assemble Transcripts
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
Side by side Base only PR only
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
short reads
ONT reads
ONT reads
HiFi reads
HiFi reads
hifiasm flye
hifiasm flye
Reference genome
Reference genome
Reference annotation
Reference annotation
hifiasm_ul
hifiasm_ul
HiC reads
HiC reads
Scaffold: ONT / HiFi
Scaffold: ONT / HiFi
fastplong
fastplong
fastp
fastp
pilon
pilon
k-mer: meryl / merqury
k-mer: meryl / merqury
medaka dorado
medaka dorado
Ref: RagTag
Ref: RagTag
longstitch LINKS
longstitch LINKS
liftoff
liftoff
QUAST
QUAST
HiC: yahs
HiC: yahs
BUSCO
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
short reads
ONT reads
ONT reads
HiFi reads
HiFi reads
hifiasm flye
hifiasm flye
Reference genome
Reference genome
Reference annotation
Reference annotation
hifiasm_ul
hifiasm_ul
HiC reads
HiC reads
Scaffold: ONT / HiFi
Scaffold: ONT / HiFi
fastplong
fastplong
fastp
fastp
pilon
pilon
k-mer: meryl / merqury
k-mer: meryl / merqury
medaka dorado
medaka dorado
Ref: RagTag
Ref: RagTag
longstitch LINKS
longstitch LINKS
liftoff
liftoff
QUAST
QUAST
HiC: yahs
HiC: yahs
BUSCO
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
Side by side Base only PR only
Base (main)
Packed multi-row grid
1
Section A
2
Section B
5
Section C
6
Section D
7
Section E
3
Section F
8
Section G
4
Section H
DATA
DATA
DATA
DATA
DATA
DATA
DATA
D1
D1
D3
D3
G1
G1
B1
B1
D5
D5
E2
E2
F3
F3
H1
H1
G2
G2
C1
C1
D6
D6
E1
E1
F1
F1
D7
D7
D2
D2
G3
G3
G4
G4
A1
A1
B2
B2
E3
E3
G5
G5
C2
C2
G6
G6
F2
F2
G7
G7
D4
D4
E4
E4
G8
G8
A2
A2
E5
E5
G9
G9
C3
C3
A3
A3
D8
D8
A4
A4
A5
A5
A6
A6
A7
A7
A8
A8
A9
A9
A10
A10
A11
A11
A12
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
Section A
2
Section B
5
Section C
6
Section D
7
Section E
3
Section F
8
Section G
4
Section H
DATA
DATA
DATA
DATA
DATA
DATA
DATA
D1
D1
D3
D3
G1
G1
B1
B1
D5
D5
E2
E2
F3
F3
H1
H1
G2
G2
C1
C1
D6
D6
E1
E1
F1
F1
D7
D7
D2
D2
G3
G3
G4
G4
A1
A1
B2
B2
E3
E3
G5
G5
C2
C2
G6
G6
F2
F2
G7
G7
D4
D4
E4
E4
G8
G8
A2
A2
E5
E5
G9
G9
C3
C3
A3
A3
D8
D8
A4
A4
A5
A5
A6
A6
A7
A7
A8
A8
A9
A9
A10
A10
A11
A11
A12
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
Side by side Base only PR only
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
Input
Normalize
Normalize
Merge Modalities
Merge Modalities
Cell Typing
Cell Typing
Aggregate
Aggregate
Normalize
Normalize
Doublet Detection
Doublet Detection
Peak Calling
Peak Calling
Demux
Demux
Cluster
Cluster
WNN
WNN
Trajectory
Trajectory
Render Report
Render Report
Quantify
Quantify
Ambient RNA
Ambient RNA
Motif Analysis
Motif Analysis
Raw QC
Raw QC
Markers
Markers
UMAP
UMAP
Gene Reg. Network
Gene Reg. Network
Visualize
Visualize
QC Metrics
QC Metrics
Footprinting
Footprinting
Trim
Trim
Trajectories
Trajectories
Coverage
Coverage
Filter
Filter
DGE
DGE
Clean QC
Clean QC
Classify
Classify
Sort
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
Input
Normalize
Normalize
Merge Modalities
Merge Modalities
Cell Typing
Cell Typing
Aggregate
Aggregate
Normalize
Normalize
Doublet Detection
Doublet Detection
Peak Calling
Peak Calling
Demux
Demux
Cluster
Cluster
WNN
WNN
Trajectory
Trajectory
Render Report
Render Report
Quantify
Quantify
Ambient RNA
Ambient RNA
Motif Analysis
Motif Analysis
Raw QC
Raw QC
Markers
Markers
UMAP
UMAP
Gene Reg. Network
Gene Reg. Network
Visualize
Visualize
QC Metrics
QC Metrics
Footprinting
Footprinting
Trim
Trim
Trajectories
Trajectories
Coverage
Coverage
Filter
Filter
DGE
DGE
Clean QC
Clean QC
Classify
Classify
Sort
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
Genomeassembly Organellar changed
Side by side Base only PR only
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
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
MitoHiFi
MitoHiFi
hifiasm
hifiasm
oatk
oatk
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
MitoHiFi
MitoHiFi
hifiasm
hifiasm
oatk
oatk
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
Side by side Base only PR only
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
BB0
BB2
BB2
AL0
AL0
BB4
BB4
FL1
FL1
FM2
FM2
Station C
Station C
RP0
RP0
BA0
BA0
BB5
BB5
FL0
FL0
FM0
FM0
Station A
Station A
BB6
BB6
BB1
BB1
T2
T2
T3
T3
PP1
PP1
AL1
AL1
FL2
FL2
T4
T4
BA1
BA1
FM1
FM1
Station B
Station B
BB3
BB3
PP2
PP2
FL3
FL3
BA2
BA2
T0
T0
T1
T1
PP3
PP3
BB7
BB7
PP4
PP4
PP5
PP5
PP6
PP6
PP7
PP7
PP8
PP8
PP9
PP9
PP10
PP10
PP11
PP11
PP12
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
BB0
BB2
BB2
AL0
AL0
BB4
BB4
FL1
FL1
FM2
FM2
Station C
Station C
RP0
RP0
BA0
BA0
BB5
BB5
FL0
FL0
FM0
FM0
Station A
Station A
BB6
BB6
BB1
BB1
T2
T2
T3
T3
PP1
PP1
AL1
AL1
FL2
FL2
T4
T4
BA1
BA1
FM1
FM1
Station B
Station B
BB3
BB3
PP2
PP2
FL3
FL3
BA2
BA2
T0
T0
T1
T1
PP3
PP3
BB7
BB7
PP4
PP4
PP5
PP5
PP6
PP6
PP7
PP7
PP8
PP8
PP9
PP9
PP10
PP10
PP11
PP11
PP12
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
Side by side Base only PR only
Base (main)
riboseq (te + psite_id excerpt)
1
Alignment
2
Extended ORF discovery & calling
4
P-site identification
3
Quantification
5
Translational efficiency
BED
ORF catalogue
HTML
riboWaltz
HTML
TE report
Ribo-TISH
Ribo-TISH
plastid P-site
plastid P-site
Plastid P-site counts
Plastid P-site counts
riboWaltz
riboWaltz
UMI-tools Dedup
UMI-tools Dedup
Salmon
Salmon
Merge ORF catalogue
Merge ORF catalogue
plastid Wiggle
plastid Wiggle
Prep TE counts
Prep TE counts
Quantify ORF P-sites
Quantify ORF P-sites
anota2seq
anota2seq
DESeq2 deltaTE
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
Alignment
2
Extended ORF discovery & calling
4
P-site identification
3
Quantification
5
Translational efficiency
BED
ORF catalogue
HTML
riboWaltz
HTML
TE report
Ribo-TISH
Ribo-TISH
plastid P-site
plastid P-site
Plastid P-site counts
Plastid P-site counts
riboWaltz
riboWaltz
UMI-tools Dedup
UMI-tools Dedup
Salmon
Salmon
Merge ORF catalogue
Merge ORF catalogue
plastid Wiggle
plastid Wiggle
Prep TE counts
Prep TE counts
Quantify ORF P-sites
Quantify ORF P-sites
anota2seq
anota2seq
DESeq2 deltaTE
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
Nf Variant Calling Tuned changed
Side by side Base only PR only
Base (main)
Variant Calling Pipeline
1
Pre-processing
2
Alignment
3
Variant Calling
4
Reporting
BWA Index
BWA Index
GATK HaplotypeCaller
GATK HaplotypeCaller
DeepVariant
DeepVariant
FastQC
FastQC
MultiQC
MultiQC
FastP
FastP
BWA-MEM
BWA-MEM
BCFtools Stats
BCFtools Stats
SAMtools Sort
SAMtools Sort
SAMtools Index
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
Pre-processing
2
Alignment
3
Variant Calling
4
Reporting
BWA Index
BWA Index
GATK HaplotypeCaller
GATK HaplotypeCaller
DeepVariant
DeepVariant
FastQC
FastQC
MultiQC
MultiQC
FastP
FastP
BWA-MEM
BWA-MEM
BCFtools Stats
BCFtools Stats
SAMtools Sort
SAMtools Sort
SAMtools Index
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
Side by side Base only PR only
Base (main)
Variant Calling Pipeline
1
Pre-processing
2
Alignment
3
Variant Calling
4
Reporting
FASTQ
FASTA
VCF
HTML
GATK HaplotypeCaller
GATK HaplotypeCaller
DeepVariant
DeepVariant
MultiQC
MultiQC
BWA Index
BWA Index
FastP
FastP
BCFtools Stats
BCFtools Stats
FastQC
FastQC
BWA-MEM
BWA-MEM
SAMtools Sort
SAMtools Sort
SAMtools Index
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
Pre-processing
2
Alignment
3
Variant Calling
4
Reporting
FASTQ
FASTA
VCF
HTML
GATK HaplotypeCaller
GATK HaplotypeCaller
DeepVariant
DeepVariant
MultiQC
MultiQC
BWA Index
BWA Index
FastP
FastP
BCFtools Stats
BCFtools Stats
FastQC
FastQC
BWA-MEM
BWA-MEM
SAMtools Sort
SAMtools Sort
SAMtools Index
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 Input Above Consumer changed
Side by side Base only PR only
Base (main)
Long-read Methylation & Variant Atlas
1
Intake & Basecall
2
Alignment
3
Methylation Calling
4
Variant Calling
5
Expression
6
Fusion Detection
7
Merge & Annotate
8
Report
FASTA
Reference
GTF
Annotation
BAM
Aligned
BED
CpG islands
bigWig
Methylation
POD5
POD5
modkit
modkit
Clair3
Clair3
Collect
Collect
Aggregate
Aggregate
IsoQuant
IsoQuant
JAFFAL
JAFFAL
Basecall
Basecall
minimap2
minimap2
Pileup
Pileup
Phase
Phase
VEP
VEP
MultiQC
MultiQC
Count
Count
Annotate
Annotate
Demux
Demux
Sort
Sort
DMR
DMR
Filter
Filter
Classify
Classify
Report
Report
Normalize
Normalize
ReadQC
ReadQC
Index
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
Intake & Basecall
2
Alignment
3
Methylation Calling
4
Variant Calling
5
Expression
6
Fusion Detection
7
Merge & Annotate
8
Report
FASTA
Reference
GTF
Annotation
BAM
Aligned
BED
CpG islands
bigWig
Methylation
POD5
POD5
modkit
modkit
Clair3
Clair3
Collect
Collect
Aggregate
Aggregate
IsoQuant
IsoQuant
JAFFAL
JAFFAL
Basecall
Basecall
minimap2
minimap2
Pileup
Pileup
Phase
Phase
VEP
VEP
MultiQC
MultiQC
Count
Count
Annotate
Annotate
Demux
Demux
Sort
Sort
DMR
DMR
Filter
Filter
Classify
Classify
Report
Report
Normalize
Normalize
ReadQC
ReadQC
Index
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
Pipeline Genomeassembly changed
Side by side Base only PR only
Base (main)
sanger-tol/genomeassembly
1
Raw assembly
2
Purging
3
Polishing
4
Scaffolding
5
Genome QC
FASTX
CRAM
FASTQ
bwa-mem2
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
Hifiasm
Hifiasm
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
Raw assembly
2
Purging
3
Polishing
4
Scaffolding
5
Genome QC
FASTX
CRAM
FASTQ
bwa-mem2
bwa-mem2
minimap2
minimap2
asmstats
asmstats
minimap2
minimap2
GFAStats
GFAStats
purge_dups
purge_dups
Longranger
Longranger
YaHS
YaHS
BUSCO
BUSCO
Hifiasm
Hifiasm
MerquryFK
MerquryFK
PretextMap
PretextMap
FreeBayes
FreeBayes
Juicer
Juicer
Cooler
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
Side by side Base only PR only
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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
Subsample
SV Processing
SV Processing
Filter Contigs
Filter Contigs
bcftools stats
bcftools stats
SURVIVOR stats
SURVIVOR stats
Truvari
Truvari
SVanalyzer
SVanalyzer
bcftools filter
bcftools filter
RTGtools bndeval
RTGtools bndeval
Samplesheet
Samplesheet
SURVIVOR merge
SURVIVOR merge
SURVIVOR filter
SURVIVOR filter
wittyer
wittyer
Reference Genome
Reference Genome
Liftover (Picard, UCSC)
Liftover (Picard, UCSC)
Variant Normalization
Variant Normalization
bcftools merge
bcftools merge
RTGtools vcfeval
RTGtools vcfeval
Truth VCF
Truth VCF
hap.py
hap.py
Regions BED
Regions BED
som.py
som.py
Targets BED
Targets BED
GATK4 Concordance
GATK4 Concordance
Merge TP/FP/FN
Merge TP/FP/FN
SNV stats
SNV stats
Intersection
Intersection
Summary Stats
Summary Stats
SV stats
SV stats
Benchmarking Summaries
Benchmarking Summaries
Consensus Filter
Consensus Filter
VCF to CSV
VCF to CSV
datavzrd
datavzrd
Merged CSVs
Merged CSVs
Plots
Plots
HTML Report
HTML Report
MultiQC Report
MultiQC Report
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
Side by side Base only PR only
Base (main)
nf-core/variantprioritization
1
Pre-processing of vcf files
2
Prepare files for PCGR
3
Reference
5
PCGR
4
CPSR
VCF
CNA
HTML
HTML
Reformat VCF
Reformat VCF
PCGR
PCGR
CPSR
CPSR
PCGR DB
PCGR DB
VEP Cache
VEP Cache
Intersect VCF
Intersect VCF
tabix
tabix
Reformat CNA
Reformat CNA
bcftools/norm
bcftools/norm
Prepare VCF
Prepare VCF
bcftools/filter
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
Pre-processing of vcf files
2
Prepare files for PCGR
3
Reference
5
PCGR
4
CPSR
VCF
CNA
HTML
HTML
Reformat VCF
Reformat VCF
PCGR
PCGR
CPSR
CPSR
PCGR DB
PCGR DB
VEP Cache
VEP Cache
Intersect VCF
Intersect VCF
tabix
tabix
Reformat CNA
Reformat CNA
bcftools/norm
bcftools/norm
Prepare VCF
Prepare VCF
bcftools/filter
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
Right Entry Over Top Tall Upstream changed
Side by side Base only PR only
Base (main)
Over-top right entry, tall upstream
1
Source
2
Tall Upstream
3
Feeder
4
Target
Prepare A
Prepare A
Step 1
Step 1
Prep C
Prep C
Merge
Merge
Prepare B
Prepare B
Step 2
Step 2
Prep D
Prep D
Report
Report
Step 3
Step 3
Step 4
Step 4
Step 5
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
Source
2
Tall Upstream
3
Feeder
4
Target
Prepare A
Prepare A
Step 1
Step 1
Prep C
Prep C
Merge
Merge
Prepare B
Prepare B
Step 2
Step 2
Prep D
Prep D
Report
Report
Step 3
Step 3
Step 4
Step 4
Step 5
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
Side by side Base only PR only
Base (main)
TB Internal Diagonal
1
Source
2
Work
Start
Start
Demux
Demux
Lane A
Lane A
End
End
Lane B
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
Source
2
Work
Start
Start
Demux
Demux
Lane A
Lane A
End
End
Lane B
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
Side by side Base only PR only
Base (main)
TB Left Exit
1
Prep
2
Work
3
Report
Start
Start
Process
Process
Publish
Publish
End
End
Collect
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
Prep
2
Work
3
Report
Start
Start
Process
Process
Publish
Publish
End
End
Collect
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
Side by side Base only PR only
Base (main)
TB Right Exit
1
Prep
2
Work
3
Report
Start
Start
Process
Process
Publish
Publish
End
End
Collect
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
Prep
2
Work
3
Report
Start
Start
Process
Process
Publish
Publish
End
End
Collect
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
Self Crossing Bridge changed
Side by side Base only PR only
Base (main)
Self-Crossing Bridge
1
Top
3
Mid Source
4
Mid Sink
2
Bus Sink
Top In
Top In
Mid In
Mid In
Mid Collect
Mid Collect
Bus Collect
Bus Collect
Top Out
Top Out
Mid Out
Mid Out
Mid Report
Mid Report
Bus 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
Top In
Mid In
Mid In
Mid Collect
Mid Collect
Bus Collect
Bus Collect
Top Out
Top Out
Mid Out
Mid Out
Mid Report
Mid Report
Bus 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