Render diff - PR #1269

5 changed out of 217 total renders. Generated 2026-07-03 13:09 UTC.

What is this page?

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

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

What to look for:

Layout-quality metrics

Advisory only — nothing gates on these. Lower is better; green improved, red regressed.

RenderCrossingsNear-horiz.Lone diag.Label strikesExcess gapsWasted canvas
funcprofiler_upstream30→31 (+1)430155%→54% (−1%)
pipeline_sarek_metro0000012%→12% (+0%)
rnaseq_sections0000018%→17% (−0%)
rnaseq_sections_manual0000018%→17% (−0%)
sarek_metro0000012%→12% (+0%)

Changed renders

Fan-out and Fan-in

nf-core Pipelines

Getting Started

Guide Examples

Realistic Pipelines

Fan-out and Fan-in

Funcprofiler Upstream changed

Base (main)

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

PR

nf-core/funcprofiler (upstream) 1 Input 2 Functional Profiling 3 Quality Check 4 Output Short Reads Input Databases HUMAnN v3 MultiQC Results Directory HUMAnN v4 FMH FunProfiler RGI mifaser DIAMOND eggNOG-mapper Preprocess MERGE_RUNS input__exit_right_0 (right) profiling__exit_right_1 (right) QC__exit_right_2 (right) profiling__entry_left_3 (left) QC__entry_left_4 (left) Output__entry_left_5 (left) __junction_6 (?) __junction_7 (?) __merge_2 (?) col 0|1 col 1|2 col 2|3 row 0 grid 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

nf-core Pipelines

Pipeline Sarek Metro changed

Base (main)

1 Pre-processing 2 Variant calling 3 Annotation 4 Example analysis pathways uBAM spring FASTQ BAM/ CRAM CRAM CRAM CRAM VCF VCF CRAM VCF TXT ... variant calling snpEff convert bcftools ensemblVEP DeepVariant FastQC samtools bcftools annotate FreeBayes UMI Varlociraptor MultiQC HaplotypeCaller finalise FastP Sentieon Haplotyper normalise BBsplit Sentieon DNAscope consensus mapping Sentieon TNscope convert LoFreq markduplicates mosdepth, samtools MuSE prepare recalibration mpileup applybqsr Mutect2 mosdepth, samtools Strelka2 NGSCheckmate indexcov Manta TIDDIT ASCAT Control-FREEC CNVkit MSIsensor2 MSIsensor-pro SNPs & Indels SV & CNV MSI preprocessing__exit_right_0 (right) variantcalling__exit_right_1 (right) variantcalling__entry_left_2 (left) annotation__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _vc_merge __converge_out_1 Core workflow Germline Tumor only Tumor-normal pair Mandatory Parabricks accelerated Sentieon accelerated Parabricks & Sentieon accelerated Expanded in pathways panel created with nf-metro v1.1.0+dev Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)

PR

1 Pre-processing 2 Variant calling 3 Annotation 4 Example analysis pathways uBAM spring FASTQ BAM/ CRAM CRAM CRAM CRAM VCF VCF CRAM VCF TXT ... variant calling snpEff convert bcftools ensemblVEP DeepVariant FastQC samtools bcftools annotate FreeBayes UMI Varlociraptor MultiQC HaplotypeCaller finalise FastP Sentieon Haplotyper normalise BBsplit Sentieon DNAscope consensus mapping Sentieon TNscope convert LoFreq markduplicates mosdepth, samtools MuSE prepare recalibration mpileup applybqsr Mutect2 mosdepth, samtools Strelka2 NGSCheckmate indexcov Manta TIDDIT ASCAT Control-FREEC CNVkit MSIsensor2 MSIsensor-pro SNPs & Indels SV & CNV MSI preprocessing__exit_right_0 (right) variantcalling__exit_right_1 (right) variantcalling__entry_left_2 (left) annotation__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _vc_merge __converge_out_1 Core workflow Germline Tumor only Tumor-normal pair Mandatory Parabricks accelerated Sentieon accelerated Parabricks & Sentieon accelerated Expanded in pathways panel created with nf-metro v1.1.0+dev Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)

Getting Started

Rnaseq Sections changed

Base (main)

1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing 5 Quality control & reporting FASTQ HTML HTML HTML STAR SAMtools RSeQC HISAT2 Bowtie2 Salmon Kallisto Cat FASTQ RSEM Picard Preseq UMI-tools Dedup tximport FastQC BEDTools Qualimap Salmon Sum. Exp. Infer Strandedness tximport bedGraphToBigWig dupRadar MultiQC MultiQC UMI-tools Extract Sum. Exp. StringTie featureCounts fastp DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken Sylph BBSplit MultiQC SortMeRNA RiboDetector FastQC preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) postprocessing__exit_bottom_2 (bottom) genome_align__entry_left_3 (left) pseudo_align__entry_left_4 (left) postprocessing__entry_left_5 (left) qc_report__entry_top_6 (top) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Aligner: Bowtie2, Quantification: Salmon Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

PR

1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing 5 Quality control & reporting FASTQ HTML HTML HTML STAR SAMtools RSeQC HISAT2 Bowtie2 Salmon Kallisto Cat FASTQ RSEM Picard Preseq UMI-tools Dedup tximport FastQC BEDTools Qualimap Salmon Sum. Exp. Infer Strandedness tximport bedGraphToBigWig dupRadar MultiQC MultiQC UMI-tools Extract Sum. Exp. StringTie featureCounts fastp DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken Sylph BBSplit MultiQC SortMeRNA RiboDetector FastQC preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) postprocessing__exit_bottom_2 (bottom) genome_align__entry_left_3 (left) pseudo_align__entry_left_4 (left) postprocessing__entry_left_5 (left) qc_report__entry_top_6 (top) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Aligner: Bowtie2, Quantification: Salmon Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

Guide Examples

Rnaseq Sections Manual changed

Base (main)

1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing 5 Quality control & reporting FASTQ HTML HTML HTML STAR SAMtools RSeQC HISAT2 Bowtie2 Salmon Kallisto cat fastq RSEM Picard Preseq UMI-tools dedup tximport FastQC BEDTools Qualimap Salmon Sum. Exp. infer strandedness tximport bedGraphToBigWig dupRadar MultiQC MultiQC UMI-tools extract Sum. Exp. StringTie featureCounts FastP DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken Sylph BBSplit MultiQC SortMeRNA RiboDetector FastQC preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) postprocessing__exit_bottom_2 (bottom) genome_align__entry_left_3 (left) pseudo_align__entry_left_4 (left) postprocessing__entry_left_5 (left) qc_report__entry_top_6 (top) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Aligner: Bowtie2, Quantification: Salmon Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

PR

1 Pre-processing 2 Genome alignment & quantification 3 Pseudo-alignment & quantification 4 Post-processing 5 Quality control & reporting FASTQ HTML HTML HTML STAR SAMtools RSeQC HISAT2 Bowtie2 Salmon Kallisto cat fastq RSEM Picard Preseq UMI-tools dedup tximport FastQC BEDTools Qualimap Salmon Sum. Exp. infer strandedness tximport bedGraphToBigWig dupRadar MultiQC MultiQC UMI-tools extract Sum. Exp. StringTie featureCounts FastP DESeq2 PCA Trim Galore! FastQC Kraken2/Bracken Sylph BBSplit MultiQC SortMeRNA RiboDetector FastQC preprocessing__exit_right_0 (right) genome_align__exit_right_1 (right) postprocessing__exit_bottom_2 (bottom) genome_align__entry_left_3 (left) pseudo_align__entry_left_4 (left) postprocessing__entry_left_5 (left) qc_report__entry_top_6 (top) __junction_7 (?) col 0|1 col 1|2 row 0|1 row 1|2 row 0 grid row 1 grid row 0 grid row 2 grid _h1 _h2 _h3 Aligner: STAR, Quantification: RSEM Aligner: STAR, Quantification: Salmon (default) Aligner: HISAT2, Quantification: None Aligner: Bowtie2, Quantification: Salmon Pseudo-aligner: Salmon, Quantification: Salmon Pseudo-aligner: Kallisto, Quantification: Kallisto created with nf-metro v1.1.0+dev

Realistic Pipelines

Sarek Metro changed

Base (main)

1 Pre-processing 2 Variant calling 3 Annotation 4 Example analysis pathways uBAM spring FASTQ BAM/ CRAM CRAM CRAM CRAM VCF VCF CRAM VCF TXT ... variant calling snpEff convert bcftools ensemblVEP DeepVariant FastQC samtools bcftools annotate FreeBayes UMI Varlociraptor MultiQC HaplotypeCaller finalise FastP Sentieon Haplotyper normalise BBsplit Sentieon DNAscope consensus mapping Sentieon TNscope convert LoFreq markduplicates mosdepth, samtools MuSE prepare recalibration mpileup applybqsr Mutect2 mosdepth, samtools Strelka2 NGSCheckmate indexcov Manta TIDDIT ASCAT Control-FREEC CNVkit MSIsensor2 MSIsensor-pro SNPs & Indels SV & CNV MSI preprocessing__exit_right_0 (right) variantcalling__exit_right_1 (right) variantcalling__entry_left_2 (left) annotation__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _vc_merge __converge_out_1 Core workflow Germline Tumor only Tumor-normal pair Mandatory Parabricks accelerated Sentieon accelerated Parabricks & Sentieon accelerated Expanded in pathways panel created with nf-metro v1.1.0+dev Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)

PR

1 Pre-processing 2 Variant calling 3 Annotation 4 Example analysis pathways uBAM spring FASTQ BAM/ CRAM CRAM CRAM CRAM VCF VCF CRAM VCF TXT ... variant calling snpEff convert bcftools ensemblVEP DeepVariant FastQC samtools bcftools annotate FreeBayes UMI Varlociraptor MultiQC HaplotypeCaller finalise FastP Sentieon Haplotyper normalise BBsplit Sentieon DNAscope consensus mapping Sentieon TNscope convert LoFreq markduplicates mosdepth, samtools MuSE prepare recalibration mpileup applybqsr Mutect2 mosdepth, samtools Strelka2 NGSCheckmate indexcov Manta TIDDIT ASCAT Control-FREEC CNVkit MSIsensor2 MSIsensor-pro SNPs & Indels SV & CNV MSI preprocessing__exit_right_0 (right) variantcalling__exit_right_1 (right) variantcalling__entry_left_2 (left) annotation__entry_left_3 (left) col 0|1 col 1|2 row 0|1 row 0 grid row 1 grid _vc_merge __converge_out_1 Core workflow Germline Tumor only Tumor-normal pair Mandatory Parabricks accelerated Sentieon accelerated Parabricks & Sentieon accelerated Expanded in pathways panel created with nf-metro v1.1.0+dev Adapted from: Fellows Yates, James A., et al. PeerJ 9 (2021)