diff --git a/assets/report/report.qmd b/assets/report/report.qmd index d1fc7992..2c257e6f 100644 --- a/assets/report/report.qmd +++ b/assets/report/report.qmd @@ -1,6 +1,6 @@ --- title: PGS Catalog Calculator (`pgsc_calc`) report -author: PGS Catalog team +author: PGS Catalog Calculator (`pgsc_calc`) date: today title-block-banner: "#383434" toc: true @@ -16,6 +16,7 @@ params: sampleset: "" run_ancestry: false reference_panel_name: "" + version: "" css: logo.css --- @@ -55,12 +56,20 @@ log_df <- Reduce(dplyr::bind_rows, lapply(log_paths, read_log)) log_df$sampleset <- gsub("_", " ", log_df$sampleset) # page breaking issues ``` -# Pipeline command +# Workflow metadata + +## Command ```{bash} cat command.txt | fold -w 80 -s | awk -F ' ' 'NR==1 { print "$", $0} NR>1 { print " " $0}' | sed 's/$/\\/' | sed '$ s/.$//' ``` +## Version + +```{r, echo=FALSE} +message(params$version) +``` + # Scoring file metadata ## Scoring file summary diff --git a/modules/local/score_report.nf b/modules/local/score_report.nf index fff3ad6b..5f4a08ea 100644 --- a/modules/local/score_report.nf +++ b/modules/local/score_report.nf @@ -35,6 +35,7 @@ process SCORE_REPORT { """ export TMPDIR=\$(mktemp -d --tmpdir=.) # tmpdir must always be writable for quarto echo $workflow.commandLine > command.txt + echo "keep_multiallelic: $params.keep_multiallelic" > params.txt echo "keep_ambiguous : $params.keep_ambiguous" >> params.txt echo "min_overlap : $params.min_overlap" >> params.txt @@ -44,6 +45,7 @@ process SCORE_REPORT { -P sampleset:$meta.id \ -P run_ancestry:$run_ancestry \ -P reference_panel_name:$reference_panel_name \ + -P version:$workflow.manifest.version \ -o report.html cat <<-END_VERSIONS > versions.yml