From 1eb951715f03cc873dc76ff788aef14da441ddb8 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 20 Apr 2023 15:57:57 +0200
Subject: [PATCH 1/2] MultiQC optimisations for DIAMOND and Falco

---
 assets/multiqc_config.yml | 3 +--
 workflows/taxprofiler.nf  | 7 ++++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index f13d775..deaf219 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -37,8 +37,7 @@ run_modules:
 
 sp:
   diamond:
-    contents: "diamond v"
-    num_lines: 10
+    fn_re: ".*.diamond.log$"
   fastqc/data:
     fn_re: ".*(fastqc|falco)_data.txt$"
   fastqc/zip:
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 25c8d76..8a9a3f3 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -270,7 +270,12 @@ workflow TAXPROFILER {
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
 
     if ( params.preprocessing_qc_tool == 'falco' ) {
-        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
+        // only mix in files acutally used by MultiQC
+        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt
+                            .map { meta, reports -> reports }
+                            .flatten()
+                            .filter { path -> path.name.endsWith('_data.txt')}
+                            .ifEmpty([]))
     } else {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
     }

From 59f31469c36b22a3b8081c44875d8856dab0890e Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 20 Apr 2023 16:01:22 +0200
Subject: [PATCH 2/2] Update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d289cb..bff1c9a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
 - [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
 - [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
+- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
 
 ### `Dependencies`