Tb Offtrack Fork Baseline

Gallery / Off-track & Rails

A `direction: TB` section with an asymmetric fork whose branch (markduplicates) overshoots the trunk toward the lift side. The off-track downward-branch test anchors its trunk baseline to the through-trunk column rather than the lift-most station, so main-trunk producers downstream of the fork keep their off-track outputs on the lift side instead of flipping them onto the beside-trunk label side (issue #1388).

Mermaid source

examples/topologies/tb_offtrack_fork_baseline.mmd

%%metro title: TB off-track fork baseline
%% Regression for #1388: in a `direction: TB` section an asymmetric fork sends
%% one branch (markduplicates) further toward the lift side than the trunk.
%% The off-track "downward branch" test derives the trunk baseline on the cross
%% axis; taking the lift-most on-track station let that fork branch become the
%% baseline, so every main-trunk producer downstream (mosdepth, applybqsr) read
%% as a branch and its off-track output flipped onto the beside-trunk label
%% side, colliding with a neighbour label.  The baseline must anchor to the
%% trunk column the through-line runs on, not the lift-most extreme.
%%metro font_scale: 1.34
%%metro line: core | Core | #2db572
%%metro line: alt | Alt | #d62728
%%metro file: samtools_out | CRAM
%%metro file: recal_out | CRAM
%%metro off_track: samtools_out
%%metro off_track: recal_out

graph LR
    subgraph prep [Pre-processing]
        %%metro direction: TB
        a[convert]
        b[FastQC]
        c[mapping]
        d1[bam convert]
        d2[markduplicates]
        h[mosdepth, samtools]
        i[prepare recalibration]
        j[applybqsr]
        k[mosdepth, samtools]
        l[NGSCheckmate]

        a -->|core| b
        b -->|core| c
        c -->|core| d1
        c -->|alt| d2
        d1 -->|core| h
        d2 -->|alt| h
        h -->|core| samtools_out
        h -->|core| i
        i -->|core| j
        j -->|core| recal_out
        j -->|core| k
        k -->|core| l
    end

CLI command

nf-metro render examples/topologies/tb_offtrack_fork_baseline.mmd -o tb_offtrack_fork_baseline.svg

Rendered map