From ea20a1cf51f7754e2b1555389641407d932e218e Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Mon, 31 Jul 2023 17:06:42 +0200
Subject: [PATCH] add input section

---
 assets/report_template.Rmd      | 42 +++++++++++++++++++++++++++++++++
 modules/local/summary_report.nf |  8 ++++++-
 workflows/ampliseq.nf           |  3 +++
 3 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd
index 1c05a17e..da681919 100644
--- a/assets/report_template.Rmd
+++ b/assets/report_template.Rmd
@@ -12,6 +12,8 @@ output:
 date: "`r Sys.Date()`"
 #bibliography: ./references.bibtex
 params:
+    # any parameter that is by default "FALSE" is used to evaluate the inclusion of a codeblock with e.g. "eval=!isFALSE(params$mqc_plot)"
+
     # report style
     css: NULL
     logo: NULL
@@ -51,6 +53,10 @@ params:
     qiime_adonis_formula: FALSE
 
     # file paths
+    metadata: FALSE
+    samplesheet: FALSE
+    fasta: FALSE
+    input: FALSE
     mqc_plot: FALSE
     ca_sum_path: FALSE
     dada_filtntrim_args: FALSE
@@ -142,6 +148,42 @@ subtitle: `r report_subtitle`
 The bioinformatics analysis pipeline [nfcore/ampliseq](https://nf-co.re/ampliseq) is used for amplicon sequencing,
 supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment of 16S, ITS, CO1 and 18S amplicons.
 
+<!-- Section on Input -->
+
+# Input
+
+Pipeline input was saved in folder [input](../input).
+
+```{r, results='asis'}
+if ( !isFALSE(params$samplesheet) ) {
+    # samplesheet input
+    cat("Sequencing data was provided in the samplesheet file `", params$samplesheet, "` that is displayed below:", sep="")
+
+    samplesheet <- read.table(file = params$samplesheet, header = TRUE, sep = "\t")
+    # Display table
+    datatable(samplesheet, options = list(
+        scrollX = TRUE,
+        scrollY = "300px",
+        paging = FALSE))
+} else if ( !isFALSE(params$fasta) ) {
+    # fasta input
+    cat("ASV/OTU sequences were provided in the fasta file `", params$fasta, "`. ", sep="")
+} else if ( !isFALSE(params$input) ) {
+    # folder input
+    cat("Sequencing data was retrieved from folder `", params$fasta, "`. ", sep="")
+}
+if ( !isFALSE(params$metadata) ) {
+    cat("Metadata associated with the sequencing data was provided in `", params$metadata, "` and is displayed below:", sep="")
+
+    metadata <- read.table(file = params$metadata, header = TRUE, sep = "\t")
+    # Display table
+    datatable(metadata, options = list(
+        scrollX = TRUE,
+        scrollY = "300px",
+        paging = FALSE))
+}
+```
+
 <!-- Section on Preprocessing -->
 
 ```{r, eval = !isFALSE(params$mqc_plot) || !isFALSE(params$dada_filtntrim_args), results='asis'}
diff --git a/modules/local/summary_report.nf b/modules/local/summary_report.nf
index 5ffe6d05..a9d2f8c6 100644
--- a/modules/local/summary_report.nf
+++ b/modules/local/summary_report.nf
@@ -1,5 +1,4 @@
 process SUMMARY_REPORT  {
-
     label 'process_low'
 
     container 'docker.io/tillenglert/ampliseq_report:latest'
@@ -20,6 +19,9 @@ process SUMMARY_REPORT  {
     path(report_template)
     path(report_styles)
     path(report_logo)
+    path(metadata)
+    path(samplesheet)
+    path(fasta)
     path(mqc_plots)
     path(ca_summary)
     val(find_truncation_values)
@@ -76,6 +78,10 @@ process SUMMARY_REPORT  {
         "workflow_manifest_version='${workflow.manifest.version}'",
         "workflow_scriptid='${workflow.scriptId.substring(0,10)}'",
         meta.single_end ? "flag_single_end=TRUE" : "",
+        metadata ? "metadata='$metadata'" : "",
+        samplesheet ? "samplesheet='$samplesheet'" : "",
+        fasta ? "fasta='$fasta'" : "",
+        !fasta && !samplesheet ? "input='$params.input'" : "",
         mqc_plots ? "mqc_plot='${mqc_plots}/svg/mqc_fastqc_per_sequence_quality_scores_plot_1.svg'" : "",
         ca_summary ?
             params.retain_untrimmed ? "flag_retain_untrimmed=TRUE,ca_sum_path='$ca_summary'" :
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index 3da0aa28..1a4d2970 100644
--- a/workflows/ampliseq.nf
+++ b/workflows/ampliseq.nf
@@ -686,6 +686,9 @@ workflow AMPLISEQ {
             ch_report_template,
             ch_report_css,
             ch_report_logo,
+            ch_metadata.ifEmpty( [] ),
+            params.input.toString().toLowerCase().endsWith("tsv") ? ch_input : [], // samplesheet input
+            is_fasta_input ? PARSE_INPUT.out.fasta.ifEmpty( [] ) : [], // fasta input
             !is_fasta_input && !params.skip_fastqc && !params.skip_multiqc ? MULTIQC.out.plots : [], //.collect().flatten().collectFile(name: "mqc_fastqc_per_sequence_quality_scores_plot_1.svg")
             !params.skip_cutadapt ? CUTADAPT_WORKFLOW.out.summary.collect().ifEmpty( [] ) : [],
             find_truncation_values,