From a1992a484a883b7bcc2531b112c2cc0f45743a3a Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Tue, 19 Dec 2023 11:08:55 +0100
Subject: [PATCH 1/4] fix error message for --input_folder

---
 subworkflows/local/parse_input.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/parse_input.nf b/subworkflows/local/parse_input.nf
index ba8aa484..ae134ae9 100644
--- a/subworkflows/local/parse_input.nf
+++ b/subworkflows/local/parse_input.nf
@@ -11,7 +11,7 @@ workflow PARSE_INPUT {
     //Check folders in folder when multiple_sequencing_runs
     folders = multiple_sequencing_runs ? "/*" : ""
     error_message = "\nCannot find any reads matching: \"${input}${folders}${extension}\"\n"
-    error_message += "Please revise the input folder (\"--input\"): \"${input}\"\n"
+    error_message += "Please revise the input folder (\"--input_folder\"): \"${input}\"\n"
     error_message += "and the input file pattern (\"--extension\"): \"${extension}\"\n"
     error_message += "*Please note: Path needs to be enclosed in quotes!*\n"
     error_message += multiple_sequencing_runs ? "If you do not have multiple sequencing runs, please do not use \"--multiple_sequencing_runs\"!\n" : "If you have multiple sequencing runs, please add \"--multiple_sequencing_runs\"!\n"

From 51ee751e0bdacf590aab29fdaf15ad4220329e06 Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Tue, 19 Dec 2023 13:30:47 +0100
Subject: [PATCH 2/4] only report input folder when it is created

---
 assets/report_template.Rmd | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd
index 264a7149..cf1fc548 100644
--- a/assets/report_template.Rmd
+++ b/assets/report_template.Rmd
@@ -181,17 +181,13 @@ supporting denoising of any amplicon and supports a variety of taxonomic databas
 
 ```{r, results='asis'}
 if ( !isFALSE(params$metadata) ) {
-    cat(paste0("
-# Data input and Metadata
-
-Pipeline input was saved to the [input](../input) directory.
-    "))
+    cat("# Data input and Metadata\n\n")
 } else {
-    cat(paste0("
-# Data input
+    cat("# Data input\n\n")
+}
 
-Pipeline input was saved in folder [input](../input).
-    "))
+if ( !isFALSE(params$metadata) || !isFALSE(params$input_samplesheet) ) {
+    cat("Pipeline input was saved in folder [input](../input).\n\n")
 }
 
 if ( !isFALSE(params$input_samplesheet) ) {

From f572fafeceb7949351bd27c90bea468d2b9a9f01 Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Tue, 19 Dec 2023 13:42:50 +0100
Subject: [PATCH 3/4] report correct cutadapt percentages for all possible
 number ranges

---
 assets/report_template.Rmd | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd
index cf1fc548..752a6b17 100644
--- a/assets/report_template.Rmd
+++ b/assets/report_template.Rmd
@@ -258,8 +258,7 @@ the denoising tool or sequences might be lost due to being labelled as PCR chime
 # import tsv
 cutadapt_summary <- read.table(file = params$cutadapt_summary, header = TRUE, sep = "\t")
 
-cutadapt_passed_col <- as.numeric(substr(
-        cutadapt_summary$cutadapt_passing_filters_percent, 1, 4))
+cutadapt_passed_col <- as.numeric( gsub("%","",cutadapt_summary$cutadapt_passing_filters_percent) )
 
 cutadapt_max_discarded <- round( 100 - min(cutadapt_passed_col), 1 )
 cutadapt_avg_passed <- round(mean(cutadapt_passed_col),1)

From 13a6e5ec988505faf21306bd2b33646a5787b43c Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Tue, 19 Dec 2023 13:48:53 +0100
Subject: [PATCH 4/4] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ecf13f13..01ccf88b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables
 - [#673](https://github.com/nf-core/ampliseq/pull/673) - Fix logic relating to generation of qiime2 taxonomy part of summary report
 - [#676](https://github.com/nf-core/ampliseq/pull/676) - Phyloseq sometimes only produced one of multiple output files
+- [#680](https://github.com/nf-core/ampliseq/pull/680) - Improved pipeline summary report & error messages
 
 ### `Dependencies`