feat(web): show what the pipeline is doing while a job runs

"running" for two and a half minutes tells the user nothing. The job page now shows a
spinner, the elapsed time, and the pipeline step Nextflow is actually on.

- the API streams the Nextflow output into jobs.log as it arrives, instead of keeping it
  only when the run dies. Writes are throttled to one every 3s, or immediately when a new
  process starts, and are skipped for a job that has already finished, so a late line
  cannot overwrite the loader's result.
- web/src/lib/progress.ts formats the elapsed time and picks the latest [PROCESS] line.
  No percentage: the pipeline cannot honestly estimate one.
- the spinner animates only under prefers-reduced-motion: no-preference.

Verified on a live run: the page showed "VEP (tiny)" for the duration, then the variant
table replaced it on success.

Tests: api 53, web 20; ruff, mypy, svelte-check clean.

web/src/routes/samples/[id]/+page.svelte

@@ -2,6 +2,7 @@
   import { onDestroy, onMount } from 'svelte';
   import { api, type Job, type VariantPage } from '$lib/api';
   import { poll } from '$lib/poll';
+  import { formatElapsed, latestStep } from '$lib/progress';
 
   const POLL_MS = 3000;
   const finished = (j: Job) => j.status === 'succeeded' || j.status === 'failed';
@@ -15,6 +16,18 @@
   let busy = $state(false);
   let error = $state<string | null>(null);
   let stopPolling: (() => void) | null = null;
+  let now = $state(Date.now());
+
+  const running = $derived(!!job && !finished(job));
+  const elapsedMs = $derived(job ? now - Date.parse(job.created_at) : 0);
+  const step = $derived(latestStep(job?.log ?? null));
+
+  // Tick the elapsed time while a run is in flight; polling refreshes the step itself.
+  $effect(() => {
+    if (!running) return;
+    const tick = setInterval(() => (now = Date.now()), 1000);
+    return () => clearInterval(tick);
+  });
 
   onMount(async () => {
     try {
@@ -79,6 +92,12 @@
 
 {#if job}
   <p>Job <span class="hgvs">{job.id.slice(0, 8)}</span>: <span class="status {job.status}">{job.status}</span></p>
+  {#if running}
+    <p class="progress" aria-live="polite">
+      <span class="spinner" aria-hidden="true"></span>
+      Annotating for {formatElapsed(elapsedMs)}{#if step} · <span class="hgvs">{step}</span>{/if}
+    </p>
+  {/if}
   {#if job.status === 'failed' && job.log}
     <pre class="hgvs" style="white-space:pre-wrap; background:white; border:1px solid var(--line); padding:0.75rem; max-height:16rem; overflow:auto">{job.log}</pre>
   {/if}