/* Nextflow workflow management — guest lecture deck
   Palette: Nextflow green #0DC09D on slate / near-black neutral. */

:root {
  --nf-green: #0DC09D;
  --nfcore-green: #24B064;
  --slate: #1E293B;
  --near-black: #0F172A;
  --off-white: #E2E8F0;
  --muted: #94A3B8;
  --amber: #F59E0B;
  --rose: #F43F5E;
  --code-bg: #0B1220;
  --code-border: #1F2937;
}

html, body, .reveal {
  background: var(--near-black);
  color: var(--off-white);
}

/* Immersive radial mesh: Nextflow green + deep indigo glows on near-black.
   Fixed to the viewport so it does not repaint per-slide during transitions. */
.reveal-viewport {
  background:
    radial-gradient(60% 55% at 18% 12%, rgba(13, 192, 157, 0.10) 0%, rgba(13, 192, 157, 0) 60%),
    radial-gradient(55% 50% at 88% 18%, rgba(99, 102, 241, 0.12) 0%, rgba(99, 102, 241, 0) 62%),
    radial-gradient(70% 60% at 78% 92%, rgba(13, 192, 157, 0.06) 0%, rgba(13, 192, 157, 0) 65%),
    var(--near-black);
  background-attachment: fixed;
}

.reveal {
  font-family: 'Inter', system-ui, sans-serif;
  font-weight: 400;
  font-size: 26px;
  letter-spacing: 0.005em;
}

.reveal .slides {
  text-align: left;
}

.reveal section {
  padding: 0.5rem 1.5rem 3rem 1.5rem;
  box-sizing: border-box;
}

.reveal h1, .reveal h2, .reveal h3, .reveal h4 {
  font-family: 'Inter', sans-serif;
  font-weight: 600;
  color: var(--off-white);
  text-transform: none;
  letter-spacing: 0;
  margin-bottom: 0.4em;
  margin-top: 0;
}

.reveal h1 { font-size: 1.9em; line-height: 1.1; }
.reveal h2 { font-size: 1.35em; line-height: 1.15; margin-bottom: 0.5em; }
.reveal h3 { font-size: 1em; color: var(--nf-green); }

.reveal a { color: var(--nf-green); text-decoration: none; }
.reveal a:hover { text-decoration: underline; }

.reveal strong { color: var(--off-white); font-weight: 600; }
.reveal em { color: var(--off-white); font-style: italic; }

.reveal ol { margin-left: 1.1em; }
.reveal li { margin: 0.35em 0; }

/* Custom green bullets for unordered lists (ordered lists keep numerals). */
.reveal ul {
  list-style: none;
  margin-left: 0.3em;
  padding-left: 0;
}
.reveal ul > li {
  position: relative;
  padding-left: 1.3em;
}
.reveal ul > li::before {
  content: "";
  position: absolute;
  left: 0.1em;
  top: 0.62em;
  width: 0.42em;
  height: 0.42em;
  border-radius: 2px;
  background: var(--nf-green);
  box-shadow: 0 0 8px rgba(13, 192, 157, 0.5);
  transform: rotate(45deg);
}
/* Nested and reset contexts where a custom bullet would be noise. */
.reveal ul.plain, .reveal .swatches, .reveal .btn-row,
.reveal .op-list, .reveal .gantt-rows {
  list-style: none;
}
.reveal ul.plain > li { padding-left: 0; }
.reveal ul.plain > li::before { content: none; }

.reveal small { font-size: 0.7em; color: var(--muted); }

.reveal code,
.reveal pre,
.reveal kbd {
  font-family: 'JetBrains Mono', 'Fira Code', ui-monospace, monospace;
}

.reveal pre {
  background: var(--code-bg);
  border: 1px solid var(--code-border);
  border-radius: 6px;
  padding: 0.7em 0.9em;
  font-size: 0.62em;
  line-height: 1.4;
  box-shadow: none;
  width: 100%;
  max-height: none;
  overflow: auto;
  margin: 0.3em 0;
}

.reveal pre code {
  display: block;
  padding: 0;
  background: transparent;
  color: var(--off-white);
  font-size: 1em;
}

.reveal :not(pre) > code {
  background: var(--code-bg);
  color: var(--nf-green);
  padding: 0.08em 0.32em;
  border-radius: 4px;
  font-size: 0.8em;
}

.reveal blockquote {
  border-left: 3px solid var(--nf-green);
  padding: 0.4em 1em;
  background: rgba(13, 192, 157, 0.05);
  color: var(--off-white);
  font-style: normal;
  box-shadow: none;
}

/* Title slide */
.title-slide {
  text-align: left;
  padding: 2rem 2rem 3rem 2rem !important;
  display: flex !important;
  flex-direction: column;
  justify-content: center;
  height: 100%;
}
.title-slide .eyebrow {
  font-size: 0.65em;
  letter-spacing: 0.18em;
  text-transform: uppercase;
  color: var(--nf-green);
  margin-bottom: 0.8em;
}
.title-slide h1 {
  font-size: 2.2em;
  margin-bottom: 0.3em;
}
.title-slide .subtitle {
  font-size: 1em;
  color: var(--muted);
  margin-bottom: 1.5em;
  max-width: 32em;
}
.title-slide .lecturer {
  font-size: 0.7em;
  color: var(--off-white);
  line-height: 1.5;
  margin-bottom: 1em;
}
.title-slide .lecturer span { color: var(--muted); }
.title-slide .kb-hint { margin-top: 0.5em; }

/* Slide footer */
.slide-footer {
  position: absolute;
  bottom: 0.6rem;
  left: 1.5rem;
  right: 1.5rem;
  display: flex;
  justify-content: space-between;
  font-size: 0.5em;
  color: var(--muted);
  letter-spacing: 0.08em;
  text-transform: uppercase;
  pointer-events: none;
}

/* Section divider slides */
.section-divider {
  display: flex !important;
  flex-direction: column;
  justify-content: center;
  height: 100%;
  min-height: 700px;
}
.section-divider .section-num {
  color: var(--nf-green);
  font-size: 0.65em;
  letter-spacing: 0.2em;
  text-transform: uppercase;
  margin-bottom: 0.6em;
}
.section-divider h1 {
  font-size: 1.9em;
  max-width: 22ch;
}
.section-divider .section-blurb {
  margin-top: 0.6em;
  color: var(--muted);
  font-size: 0.85em;
  max-width: 40ch;
}

/* Two-column layout */
.two-col {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1.5rem;
  align-items: start;
}
.three-col {
  display: grid;
  grid-template-columns: 1fr 1fr 1fr;
  gap: 1rem;
}

/* Grid items must be allowed to shrink below their intrinsic content width,
   otherwise long pre blocks blow out the column. */
.two-col > .col,
.three-col > .col {
  min-width: 0;
}
.two-col > .col > pre,
.three-col > .col > pre {
  min-width: 0;
  box-sizing: border-box;
}

.col h3 { margin-top: 0; }

/* Comparison table */
.compare {
  width: 100%;
  border-collapse: collapse;
  font-size: 0.6em;
}
.compare th, .compare td {
  text-align: left;
  padding: 0.45em 0.6em;
  border-bottom: 1px solid var(--code-border);
}
.compare th {
  color: var(--nf-green);
  font-weight: 600;
  background: rgba(13, 192, 157, 0.06);
}
.compare td.good { color: var(--nf-green); }
.compare td.bad { color: var(--rose); }
.compare td.mid { color: var(--amber); }

/* Callouts */
.callout {
  border-left: 3px solid var(--nf-green);
  background: rgba(13, 192, 157, 0.06);
  padding: 0.6em 0.9em;
  border-radius: 0 4px 4px 0;
  font-size: 0.7em;
  color: var(--off-white);
}
.callout.warn {
  border-left-color: var(--amber);
  background: rgba(245, 158, 11, 0.06);
}
.callout.nfcore {
  border-left-color: var(--nfcore-green);
  background: rgba(36, 176, 100, 0.06);
}

/* Buttons / tabs */
.btn {
  background: rgba(15, 23, 42, 0.55);
  color: var(--off-white);
  border: 1px solid var(--code-border);
  padding: 0.45em 0.9em;
  border-radius: 5px;
  font-family: 'Inter', sans-serif;
  font-size: 0.55em;
  letter-spacing: 0.04em;
  cursor: pointer;
  transition: border-color 0.18s ease, background 0.18s ease,
              color 0.18s ease, transform 0.12s ease, box-shadow 0.18s ease;
}
.btn:hover {
  border-color: var(--nf-green);
  color: var(--nf-green);
  transform: translateY(-1px);
  box-shadow: 0 4px 14px rgba(13, 192, 157, 0.18);
}
.btn:active {
  transform: translateY(0);
  box-shadow: none;
}
.btn.active {
  border-color: var(--nf-green);
  color: var(--near-black);
  background: var(--nf-green);
  box-shadow: 0 2px 12px rgba(13, 192, 157, 0.35);
}
.btn-row {
  display: flex;
  gap: 0.5rem;
  flex-wrap: wrap;
  margin: 0.5em 0;
}

/* DAG widget */
.dag-widget {
  display: grid;
  grid-template-columns: 2fr 1fr;
  gap: 1rem;
  align-items: start;
}
.dag-stage {
  background: rgba(11, 18, 32, 0.7);
  border: 1px solid rgba(255, 255, 255, 0.05);
  border-radius: 10px;
  padding: 0.6em;
  box-shadow: 0 6px 22px rgba(0, 0, 0, 0.3);
}
.dag-svg { width: 100%; height: 360px; display: block; }
.dag-side {
  font-size: 0.6em;
  background: rgba(15, 23, 42, 0.65);
  border: 1px solid rgba(255, 255, 255, 0.06);
  border-radius: 10px;
  padding: 0.7em 0.9em;
  min-height: 360px;
  box-shadow: 0 8px 30px rgba(0, 0, 0, 0.35);
  backdrop-filter: blur(10px);
  -webkit-backdrop-filter: blur(10px);
}
.dag-side h3 {
  font-size: 1.1em;
  margin: 0 0 0.4em 0;
  color: var(--nf-green);
}
.dag-side .channel {
  font-family: 'JetBrains Mono', monospace;
  color: var(--off-white);
  background: var(--near-black);
  padding: 0.4em 0.6em;
  border-radius: 4px;
  border: 1px solid var(--code-border);
  margin-top: 0.5em;
  word-break: break-all;
  font-size: 0.95em;
}

/* SVG node styles */
.dag-svg .node rect {
  fill: var(--code-bg);
  stroke: var(--code-border);
  stroke-width: 1.5;
  transition: fill 0.25s, stroke 0.25s;
}
.dag-svg .node text {
  fill: var(--off-white);
  font-family: 'JetBrains Mono', monospace;
  font-size: 11px;
  text-anchor: middle;
  dominant-baseline: middle;
}
.dag-svg .node.active rect {
  fill: rgba(13, 192, 157, 0.18);
  stroke: var(--nf-green);
  stroke-width: 2;
}
.dag-svg .node.done rect {
  stroke: var(--nfcore-green);
}
.dag-svg .edge {
  stroke: var(--code-border);
  stroke-width: 1.5;
  fill: none;
  transition: stroke 0.25s;
}
.dag-svg .edge.active {
  stroke: var(--nf-green);
  stroke-width: 2.5;
}

/* Morph widget */
.morph-widget {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1rem;
}
.morph-widget pre { margin: 0; font-size: 0.5em; }
.morph-widget h3 {
  font-size: 0.75em;
  margin: 0 0 0.4em 0;
  color: var(--muted);
  letter-spacing: 0.08em;
  text-transform: uppercase;
}

/* Channel operator playground */
.op-widget {
  display: grid;
  grid-template-columns: 1fr 2fr;
  gap: 1rem;
}
.op-list {
  display: flex;
  flex-direction: column;
  gap: 0.4em;
}
.marble {
  background: rgba(15, 23, 42, 0.65);
  border: 1px solid rgba(255, 255, 255, 0.06);
  border-radius: 10px;
  padding: 0.7em;
  min-height: 240px;
  box-shadow: 0 8px 30px rgba(0, 0, 0, 0.35);
  backdrop-filter: blur(10px);
  -webkit-backdrop-filter: blur(10px);
}
.marble svg { width: 100%; height: 200px; }
.marble .op-desc {
  font-size: 0.55em;
  color: var(--muted);
  margin-top: 0.4em;
}
.marble .marble-node {
  fill: var(--nf-green);
}
.marble .marble-node.alt {
  fill: var(--nfcore-green);
}
.marble .marble-node.warn {
  fill: var(--amber);
}
.marble .marble-text {
  fill: var(--near-black);
  font-family: 'JetBrains Mono', monospace;
  font-size: 10px;
  text-anchor: middle;
  dominant-baseline: middle;
  font-weight: 600;
}
.marble .marble-axis {
  stroke: var(--code-border);
  stroke-width: 1;
}
.marble .marble-label {
  fill: var(--muted);
  font-family: 'JetBrains Mono', monospace;
  font-size: 10px;
}

/* Editor widget */
.editor-widget { display: grid; grid-template-columns: 1fr 1fr; gap: 1rem; }
.editor-widget .CodeMirror {
  height: 280px;
  font-family: 'JetBrains Mono', monospace;
  font-size: 12px;
  border: 1px solid var(--code-border);
  border-radius: 6px;
  background: var(--code-bg);
}
.editor-preview {
  background: rgba(11, 18, 32, 0.7);
  border: 1px solid rgba(255, 255, 255, 0.05);
  border-radius: 10px;
  padding: 0.7em;
  font-family: 'JetBrains Mono', monospace;
  font-size: 12px;
  white-space: pre-wrap;
  overflow: auto;
  height: 280px;
  color: var(--off-white);
}
.editor-preview .param { color: var(--nf-green); }

/* Executor tabs */
.executor-widget pre { font-size: 0.55em; }

/* Resume simulator */
.resume-widget {
  display: grid;
  grid-template-columns: 1fr 1fr;
  gap: 1rem;
}
.resume-col {
  background: rgba(11, 18, 32, 0.7);
  border: 1px solid rgba(255, 255, 255, 0.05);
  border-radius: 10px;
  padding: 0.6em 0.8em;
  font-size: 0.55em;
  box-shadow: 0 6px 22px rgba(0, 0, 0, 0.3);
}
.resume-col h3 { margin-top: 0; font-size: 1.05em; }
.resume-step {
  display: flex;
  justify-content: space-between;
  padding: 0.25em 0;
  border-bottom: 1px dashed var(--code-border);
  font-family: 'JetBrains Mono', monospace;
}
.resume-step:last-child { border-bottom: none; }
.tag {
  font-size: 0.85em;
  padding: 0.05em 0.5em;
  border-radius: 999px;
  letter-spacing: 0.04em;
}
.tag.run { background: var(--nf-green); color: var(--near-black); }
.tag.cache { background: var(--code-border); color: var(--muted); }
.tag.skipped { background: rgba(245, 158, 11, 0.18); color: var(--amber); }

/* Speaker overlay hint */
.kb-hint {
  font-size: 0.4em;
  color: var(--muted);
  letter-spacing: 0.08em;
  text-transform: uppercase;
}

/* Palette swatch slide */
.swatches { display: flex; gap: 0.75rem; flex-wrap: wrap; margin-top: 0.5em; }
.swatch {
  width: 7.5em;
  height: 5em;
  border-radius: 6px;
  display: flex;
  align-items: flex-end;
  padding: 0.4em 0.5em;
  font-family: 'JetBrains Mono', monospace;
  font-size: 0.5em;
  color: var(--off-white);
  border: 1px solid var(--code-border);
}
.swatch.dark { color: var(--off-white); }
.swatch.light { color: var(--near-black); }

/* Section number chip */
.chip {
  display: inline-block;
  font-size: 0.45em;
  letter-spacing: 0.16em;
  text-transform: uppercase;
  color: var(--nf-green);
  border: 1px solid rgba(13, 192, 157, 0.5);
  padding: 0.15em 0.55em;
  border-radius: 999px;
  margin-bottom: 0.6em;
}

/* Accessibility: focus rings */
.btn:focus-visible,
.reveal a:focus-visible {
  outline: 2px solid var(--nf-green);
  outline-offset: 2px;
}

/* Print / projector tweaks */
@media (max-width: 1366px) {
  .reveal { font-size: 26px; }
}

/* ============================================================
   Animated channel marbles
   Marbles fade/scale in; output-row marbles slide down from the
   input axis (per-element --dy set in app.js), reading as data
   flowing down the timelines. Replays on every tab switch / restart.
   ============================================================ */
.marble svg .marble-node,
.marble svg .marble-text {
  transform-box: fill-box;
  transform-origin: center;
}
@keyframes marbleIn {
  from { opacity: 0; transform: scale(0.35); }
  to   { opacity: 1; transform: scale(1); }
}
@keyframes marbleDrop {
  from { opacity: 0; transform: translateY(var(--dy, -42px)) scale(0.7); }
  60%  { opacity: 1; }
  to   { opacity: 1; transform: translateY(0) scale(1); }
}
.op-controls {
  display: flex;
  align-items: center;
  gap: 0.5rem;
  margin-top: 0.6em;
}
.op-controls .hint {
  font-size: 0.5em;
  color: var(--muted);
  letter-spacing: 0.04em;
}

/* Status badges — scannable component states */
.badge {
  display: inline-block;
  font-family: 'JetBrains Mono', monospace;
  font-size: 0.78em;
  font-weight: 600;
  letter-spacing: 0.03em;
  padding: 0.1em 0.55em;
  border-radius: 999px;
  border: 1px solid transparent;
  vertical-align: middle;
}
.badge-queue  { background: rgba(99, 102, 241, 0.16);  color: #A5B4FC; border-color: rgba(99,102,241,0.4); }
.badge-value  { background: rgba(245, 158, 11, 0.16);  color: var(--amber); border-color: rgba(245,158,11,0.4); }
.badge-nfcore { background: rgba(36, 176, 100, 0.16);  color: #6EE7A8; border-color: rgba(36,176,100,0.45); }
.badge-local  { background: rgba(13, 192, 157, 0.16);  color: var(--nf-green); border-color: rgba(13,192,157,0.45); }

/* Samplesheet selector tabs (live editor) */
.ss-tabs { display: flex; gap: 0.5rem; margin-bottom: 0.5em; }

/* Executor config-delta panel */
.exec-delta {
  margin-top: 0.5em;
  font-size: 0.5em;
  background: rgba(11, 18, 32, 0.7);
  border: 1px solid rgba(255, 255, 255, 0.05);
  border-left: 3px solid var(--nf-green);
  border-radius: 0 8px 8px 0;
  padding: 0.6em 0.9em;
}
.exec-delta h4 {
  margin: 0 0 0.3em 0;
  font-size: 1.05em;
  color: var(--nf-green);
  letter-spacing: 0.05em;
  text-transform: uppercase;
}
.exec-delta ul { margin: 0; }
.exec-delta li { margin: 0.15em 0; color: var(--off-white); }
.exec-delta code { font-size: 0.95em; }
.exec-delta .none { color: var(--muted); font-style: italic; }

/* Gantt timeline mockup */
.gantt-widget { display: grid; grid-template-columns: 2fr 1fr; gap: 1rem; align-items: start; }
.gantt-chart {
  background: rgba(15, 23, 42, 0.65);
  border: 1px solid rgba(255, 255, 255, 0.06);
  border-radius: 10px;
  padding: 0.7em 0.9em;
  box-shadow: 0 8px 30px rgba(0, 0, 0, 0.35);
}
.gantt-chart svg { width: 100%; height: 300px; display: block; }
.gantt-bar { cursor: pointer; transition: opacity 0.15s; }
.gantt-bar rect {
  rx: 4; ry: 4;
  fill: rgba(13, 192, 157, 0.35);
  stroke: var(--nf-green);
  stroke-width: 1;
  transition: fill 0.18s, stroke 0.18s;
  transform-box: fill-box;
  transform-origin: left center;
  animation: ganttGrow 0.6s ease both;
}
@keyframes ganttGrow { from { transform: scaleX(0); } to { transform: scaleX(1); } }
.gantt-bar:hover rect,
.gantt-bar.active rect { fill: var(--nf-green); }
.gantt-bar.active rect { stroke-width: 2; }
.gantt-label {
  fill: var(--off-white);
  font-family: 'JetBrains Mono', monospace;
  font-size: 11px;
  dominant-baseline: middle;
}
.gantt-grid { stroke: var(--code-border); stroke-width: 1; }
.gantt-tick {
  fill: var(--muted);
  font-family: 'JetBrains Mono', monospace;
  font-size: 9px;
  text-anchor: middle;
}
.gantt-info {
  background: rgba(11, 18, 32, 0.7);
  border: 1px solid rgba(255, 255, 255, 0.05);
  border-radius: 10px;
  padding: 0.8em 0.9em;
  font-size: 0.6em;
  min-height: 300px;
}
.gantt-info h3 { font-size: 1.15em; margin: 0 0 0.5em 0; color: var(--nf-green); }
.gantt-info .metric { display: flex; justify-content: space-between; padding: 0.3em 0; border-bottom: 1px dashed var(--code-border); }
.gantt-info .metric:last-child { border-bottom: none; }
.gantt-info .metric span:last-child { font-family: 'JetBrains Mono', monospace; color: var(--off-white); }

/* Seqera dashboard mockup */
.seqera-dash {
  background: rgba(15, 23, 42, 0.65);
  border: 1px solid rgba(255, 255, 255, 0.06);
  border-radius: 10px;
  padding: 0.9em 1em;
  box-shadow: 0 8px 30px rgba(0, 0, 0, 0.35);
  font-size: 0.62em;
}
.seqera-dash .dash-head {
  display: flex; align-items: center; gap: 0.5em;
  margin-bottom: 0.7em; color: var(--muted);
  font-family: 'JetBrains Mono', monospace; font-size: 0.95em;
}
.seqera-dash .live-dot {
  width: 0.6em; height: 0.6em; border-radius: 999px;
  background: var(--nf-green); box-shadow: 0 0 8px var(--nf-green);
  animation: livePulse 1.8s ease-in-out infinite;
}
@keyframes livePulse { 0%,100% { opacity: 1; } 50% { opacity: 0.35; } }
.seqera-dash .progress-label { display: flex; justify-content: space-between; margin-bottom: 0.3em; }
.seqera-dash .progress-track {
  height: 0.7em; border-radius: 999px; background: var(--code-bg);
  border: 1px solid var(--code-border); overflow: hidden;
}
.seqera-dash .progress-fill {
  height: 100%; border-radius: 999px;
  background: linear-gradient(90deg, var(--nfcore-green), var(--nf-green));
  width: 0; animation: barFill 1.4s ease both;
}
@keyframes barFill { from { width: 0; } to { width: var(--pct, 70%); } }
.seqera-dash .dials { display: grid; grid-template-columns: 1fr 1fr 1fr; gap: 0.6em; margin-top: 0.9em; }
.seqera-dash .dial { text-align: center; }
.seqera-dash .dial svg { width: 100%; height: 78px; }
.seqera-dash .dial .ring-bg { fill: none; stroke: var(--code-border); stroke-width: 7; }
.seqera-dash .dial .ring-fg {
  fill: none; stroke: var(--nf-green); stroke-width: 7; stroke-linecap: round;
  transform: rotate(-90deg); transform-origin: center;
  animation: ringFill 1.3s ease both;
}
@keyframes ringFill { from { stroke-dashoffset: var(--circ, 220); } to { stroke-dashoffset: var(--off, 60); } }
.seqera-dash .dial .ring-val {
  fill: var(--off-white); font-family: 'JetBrains Mono', monospace;
  font-size: 13px; text-anchor: middle; dominant-baseline: middle;
}
.seqera-dash .dial .dial-cap { color: var(--muted); font-size: 0.85em; letter-spacing: 0.04em; }

/* Respect reduced-motion: keep everything, just stop the motion. */
@media (prefers-reduced-motion: reduce) {
  .marble svg .marble-node,
  .marble svg .marble-text,
  .gantt-bar rect,
  .seqera-dash .progress-fill,
  .seqera-dash .dial .ring-fg,
  .seqera-dash .live-dot {
    animation: none !important;
  }
  .seqera-dash .progress-fill { width: var(--pct, 70%); }
  .seqera-dash .dial .ring-fg { stroke-dashoffset: var(--off, 60); }
}