{.section common}

# {project_name}

{.section run_section} Post-processing was started {run_date}
{.section suite_version} {suite_version}
{.end} {.section program_versions} {program_versions}
{.or} {.end} {.or} {.end}
{.section basecalls} {contents}
{.end} {.section raw_fastqc} {contents}
{.end} {.section fastqc} {contents} {.or} {.end}
{.section targ_qc}

#### Alignment and Capture

{.or} {.end} {.section pre_targ_qc} {contents}
{.end} {.section targ_qc} {contents} {.or} {.end}
{.section gene_counts}

#### Gene expression

{contents} / {.or} {.end} {.section exon_counts} {contents}
{.or} {.end} {.section gene_tpm} {contents} / {.or} {.end} {.section isoform_tpm} {contents} {.or} {.end}
{.section qc_report}

#### Summary

{contents}
{.or} {.end}
{.section mutations}

#### Variants

{contents} {.or} {.end} {.section mutations_for_single_samples} {contents}
{.or} {.end} {.section mutations_for_paired_samples} {contents} {.or} {.end} {.section oncoprints}
{oncoprints_link}
{.end}
{.end}
{.section main}

{.repeated section metric_names}
{.end}
Sample | {@}
--- | ---
{.repeated section sample_reports}
{.repeated section records}
{.end}
{sample_name} | {contents}
{.end}

{.end}
{.section sample_match_on_hover_js}{sample_match_on_hover_js}{.or}{.end}