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Improved pipeline summary report & error message #680

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merged 5 commits into from
Dec 19, 2023
Merged

Improved pipeline summary report & error message #680

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a1992a4
fix error message for --input_folder
d4straub Dec 19, 2023
51ee751
only report input folder when it is created
d4straub Dec 19, 2023
f572faf
report correct cutadapt percentages for all possible number ranges
d4straub Dec 19, 2023
13a6e5e
update changelog
d4straub Dec 19, 2023
f1ae7cb
Merge branch 'dev' into fix-report
d4straub Dec 19, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#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
- [#679](https://github.com/nf-core/ampliseq/pull/679) - Prevent masking low complexity regions by VSEARCH with lower case letters
- [#680](https://github.com/nf-core/ampliseq/pull/680) - Improved pipeline summary report & error messages

### `Dependencies`

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17 changes: 6 additions & 11 deletions assets/report_template.Rmd
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Expand Up @@ -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$input_samplesheet) ) {
Expand Down Expand Up @@ -262,8 +258,7 @@ the denoising tool or sequences might be lost due to being labelled as PCR chime
# import tsv
cutadapt_summary <- read.table(file = params$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)
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2 changes: 1 addition & 1 deletion subworkflows/local/parse_input.nf
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Expand Up @@ -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"
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