/* Fix underlines on YAML and other non-R code blocks in docs pages */
/* These appear because downlit wraps lines in <a class="sourceLine"> anchor tags */
.sourceLine {
  text-decoration: none !important;
}

/* Also ensure the anchor inherits color from parent (code highlighting) */
.sourceLine:hover {
  text-decoration: none !important;
}

.scrollable-table {
  width: 100%;
  overflow-x: auto;
  margin: 1rem 0;
}

.scrollable-table table {
  margin-bottom: 0;
  white-space: nowrap;
}


.template-article h2 {
  font-size: 1.6rem;
  font-weight: bold;
}
.template-article h3 {
  font-size: 1.6rem;
  font-weight: normal;
  border-top: 4px solid #d9d9d9;
  padding-top: 0.8rem;
  margin-top: 2rem;
}

.output-gallery-grid {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(260px, 1fr));
  gap: 1rem;
  margin: 1rem 0 2rem;
}

.output-gallery-card {
  border: 1px solid #d9d9d9;
  border-radius: 6px;
  padding: 1rem;
  background: #fff;
}

.output-gallery-card img,
.output-gallery-placeholder {
  width: 100%;
  aspect-ratio: 4 / 3;
  object-fit: contain;
  border: 1px solid #e5e5e5;
  border-radius: 4px;
  background: #f7f7f7;
}

.output-gallery-placeholder {
  display: flex;
  align-items: center;
  justify-content: center;
  color: #666;
  font-size: 0.95rem;
}

.output-gallery-title {
  margin-top: 0.8rem;
  font-size: 1.1rem;
  font-weight: 600;
}

.output-gallery-target {
  font-size: 0.85rem;
  word-break: break-word;
}

/* Manifest-driven parameter reference, shared by the three analysis guides. */
.parameter-overview {
  --parameter-ink: #183344;
  --parameter-muted: #536674;
  --parameter-line: #d5dfe5;
  --parameter-accent: #165b73;
  margin: 1.5rem 0 2rem;
  color: var(--parameter-ink);
  font-size: .9rem;
  line-height: 1.55;
}
.parameter-overview *, .parameter-overview *::before, .parameter-overview *::after { box-sizing: border-box; }
.parameter-overview-toolbar { display: grid; grid-template-columns: minmax(0, 2fr) minmax(0, 1fr); gap: 1rem; }
.parameter-overview label { display: grid; gap: .4rem; font-size: .8rem; font-weight: 600; min-width: 0; }
.parameter-overview input, .parameter-overview select {
  width: 100%; min-width: 0; min-height: 44px; border: 1px solid #aabcc7; border-radius: 6px;
  background: #fff; color: var(--parameter-ink); padding: .65rem .8rem; font: inherit; font-size: .9rem;
}
.parameter-overview :is(input, select, button, summary):focus-visible { outline: 3px solid #387e99; outline-offset: 3px; }
.parameter-filter-bar { display: flex; align-items: center; justify-content: space-between; gap: .75rem; flex-wrap: wrap; margin: 1rem 0 .75rem; }
.parameter-filter-group { display: flex; flex-wrap: wrap; gap: .4rem; }
.parameter-overview button { cursor: pointer; font: inherit; }
.parameter-filter {
  display: inline-flex; gap: .5rem; align-items: center; min-height: 40px; padding: .45rem .7rem;
  border: 1px solid var(--parameter-line); border-radius: 5px; color: var(--parameter-muted); background: #fff; font-size: .8rem !important;
}
.parameter-filter span { font-variant-numeric: tabular-nums; font-size: .75rem; }
.parameter-filter.is-active { color: #fff; background: var(--parameter-accent); border-color: var(--parameter-accent); }
.parameter-filter:hover:not(.is-active) { background: #eef5f7; }
.parameter-reset { border: 0; background: none; padding: .5rem 0; color: var(--parameter-accent); text-decoration: underline; font-size: .8rem !important; }
.parameter-overview-help { font-size: .8rem; color: var(--parameter-muted); margin: 0 0 1rem; max-width: 80ch; }
.parameter-overview-summary { margin: 0; border-top: 1px solid var(--parameter-line); padding-top: .85rem; color: var(--parameter-muted); font-size: .8rem; }
.parameter-topic { margin-top: 1.5rem; }
.parameter-topic h4 { display: flex; gap: .6rem; align-items: baseline; margin: 0 0 .6rem; border: 0; font-size: 1rem; font-weight: 650; }
.parameter-topic h4 span { font-size: .75rem; font-weight: 400; color: var(--parameter-muted); }
.parameter-list { border-top: 1px solid var(--parameter-line); }
.parameter-row { border-bottom: 1px solid var(--parameter-line); margin: 0; }
.parameter-head { position: relative; display: grid; grid-template-columns: minmax(0, 1fr) minmax(100px, .32fr); gap: .4rem 1.25rem; padding: 1rem 1.6rem 1rem .25rem; cursor: pointer; list-style: none; }
.parameter-head::-webkit-details-marker { display: none; }
.parameter-head::after { content: '+'; position: absolute; right: .3rem; top: 1rem; font-size: 1.1rem; color: var(--parameter-accent); }
.parameter-row[open] > summary::after { content: '−'; }
.parameter-head:hover { background: #f5f9fa; }
.parameter-name-wrap { display: flex; align-items: flex-start; gap: .5rem; flex-wrap: wrap; min-width: 0; }
.parameter-overview code { color: var(--parameter-ink); background: transparent; padding: 0; white-space: normal; overflow-wrap: anywhere; }
.parameter-name { font-size: .84rem; font-weight: 600; line-height: 1.6; }
.parameter-status { padding: .1rem .4rem; font-size: .65rem; border-radius: 3px; background: #edf1f4; color: #485e6d; line-height: 1.6; }
.parameter-status.required { background: #fcece3; color: #8a3e17; }
.parameter-status.defaulted { background: #e6f1ed; color: #285e4b; }
.parameter-default { display: grid; align-content: start; gap: .2rem; font-size: .8rem; }
.parameter-default > span { font-size: .65rem; text-transform: uppercase; letter-spacing: .04em; color: var(--parameter-muted); }
.parameter-default code { font-size: .8rem; }
.parameter-description { grid-column: 1 / -1; font-size: .85rem; color: var(--parameter-muted); line-height: 1.6; }
.parameter-details { display: grid; grid-template-columns: minmax(0, 1fr) minmax(0, 1fr); gap: 1rem 1.5rem; background: #f1f6f8; margin: 0 0 .8rem; padding: 1rem; border-radius: 4px; }
.parameter-detail { min-width: 0; }
.parameter-detail dt { font-size: .7rem; color: var(--parameter-muted); font-weight: 600; margin-bottom: .25rem; }
.parameter-detail dd { margin: 0; font-size: .85rem; overflow-wrap: anywhere; }
.parameter-detail code { font-size: .8rem; }
.parameter-empty-state { padding: 2rem 1rem; background: #f1f6f8; color: var(--parameter-muted); text-align: center; }
.parameter-overview-standalone { margin: 0; background: #fff; font-family: system-ui, sans-serif; }
.parameter-overview-standalone main { max-width: 960px; margin: auto; padding: 2rem; }
@media (max-width: 600px) {
  .parameter-overview-toolbar, .parameter-head, .parameter-details { grid-template-columns: minmax(0, 1fr); }
  .parameter-default { display: flex; align-items: baseline; gap: .5rem; }
  .parameter-filter { min-height: 44px; }
  .parameter-head { gap: .6rem; }
}
@media print {
  .parameter-overview-toolbar, .parameter-filter-bar { display: none; }
  .parameter-details { display: grid !important; }
}

.output-gallery-card { scroll-margin-top: 5rem; }
.output-gallery-card:target { border-color: #2761e3; box-shadow: 0 0 0 3px rgba(39,97,227,.18); }

.gem-well-overview,
.demo-donor-table {
  width: 100%;
  margin: 1rem 0 1.5rem;
  overflow-x: auto;
  border-top: 1px solid #d8dee8;
  border-bottom: 1px solid #d8dee8;
}

.demo-donor-table {
  max-width: 760px;
}

.gem-well-overview table,
.demo-donor-table table {
  width: max-content;
  min-width: 100%;
  margin-bottom: 0;
  border-collapse: separate;
  border-spacing: 1.25rem 0;
  font-size: 0.84rem;
}

.gem-well-overview caption,
.demo-donor-table caption {
  padding: 0.6rem 0;
  color: inherit;
  caption-side: top;
  font-weight: 650;
  text-align: left;
}

.gem-well-overview th,
.gem-well-overview td,
.demo-donor-table th,
.demo-donor-table td {
  padding: 0.55rem 0;
  border: 0;
  vertical-align: top;
}

.gem-well-overview thead th,
.demo-donor-table thead th {
  background: transparent;
  color: inherit;
}

.gem-well-overview thead th {
  position: relative;
  z-index: 2;
  min-width: 175px;
  max-width: 260px;
}

.gem-well-overview tbody td {
  min-width: 175px;
  max-width: 320px;
}

.tsv-required-column,
.tsv-required-column code {
  font-weight: 700;
}

.gem-well-overview th code,
.gem-well-overview td code,
.demo-donor-table th code,
.demo-donor-table td code {
  padding: 0;
  background: transparent !important;
  color: inherit !important;
  white-space: normal;
  overflow-wrap: anywhere;
}

.gem-well-column-heading {
  display: flex;
  align-items: center;
  gap: 0.4rem;
}

.gem-well-tooltip {
  position: relative;
  display: inline-flex;
}

.gem-well-tooltip button {
  display: inline-flex;
  align-items: center;
  justify-content: center;
  width: 1.15rem;
  height: 1.15rem;
  padding: 0;
  border: 1px solid #8391a2;
  border-radius: 999px;
  background: #fff;
  color: #455468;
  cursor: help;
  font-family: Georgia, serif;
  font-size: 0.75rem;
  font-weight: 700;
}

.gem-well-tooltip button:focus-visible {
  outline: 3px solid rgba(39, 97, 227, 0.22);
  outline-offset: 2px;
}

.gem-well-tooltip [role="tooltip"] {
  position: absolute;
  top: calc(100% + 0.35rem);
  left: -0.35rem;
  z-index: 6;
  display: none;
  width: 300px;
  padding: 0.55rem 0.65rem;
  border-radius: 5px;
  background: #172033;
  color: #fff;
  font-size: 0.76rem;
  font-weight: 400;
  line-height: 1.4;
  box-shadow: 0 4px 14px rgba(16, 32, 39, 0.2);
}

.gem-well-tooltip:hover [role="tooltip"],
.gem-well-tooltip:focus-within [role="tooltip"] {
  display: block;
}

.gem-well-QC-value {
  display: block;
  min-width: 360px;
}