From e4b0df553a57160188206b50dbb02bae87a9ad78 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Tue, 8 Oct 2024 16:33:52 +1300
Subject: [PATCH] Added Gffcompare to multiqc and patched up the config file

---
 CHANGELOG.md              |  2 ++
 assets/multiqc_config.yml | 14 +++++++-------
 conf/modules.config       |  1 +
 workflows/genepal.nf      |  2 ++
 4 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bc653bc..a97b131 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+1. Now using `${meta.id}_trim` as prefix for `FASTQC` files
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 67df9ee..f1d666d 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -15,15 +15,14 @@ disable_version_detection: true
 module_order:
   - fastqc:
       name: "FastQC (raw)"
-      info: "This section of the report shows FastQC results before adapter trimming."
-      path_filters:
-        - "*_raw*fastqc.zip"
-  - fastp
+      path_filters_exclude:
+        - "*_trim*"
+  - fastp:
   - fastqc:
-      name: "FastQC (trimmed)"
-      info: "This section of the report shows FastQC results after adapter trimming."
+      name: "FastQC (trim)"
       path_filters:
-        - "*_trim*fastqc.zip"
+        - "*_trim*"
+  - star:
   - busco:
       name: "BUSCO"
       info: "Genome completeness statistics"
@@ -34,6 +33,7 @@ module_order:
       info: "Annotation completeness statistics"
       path_filters_exclude:
         - "*seqkit.rmdup.fasta.txt"
+  - gffcompare:
 
 extra_fn_clean_exts:
   - ".seqkit"
diff --git a/conf/modules.config b/conf/modules.config
index 2c7ff8e..c72895e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -81,6 +81,7 @@ process { // SUBWORKFLOW: PREPROCESS_RNASEQ
 
         withName: '.*:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
             ext.args   = '--quiet'
+            ext.prefix = { "${meta.id}_trim" }
             publishDir = [
                 path: { "${params.outdir}/fastqc_trim" },
                 mode: params.publish_dir_mode,
diff --git a/workflows/genepal.nf b/workflows/genepal.nf
index 7cc3226..15042f6 100644
--- a/workflows/genepal.nf
+++ b/workflows/genepal.nf
@@ -258,6 +258,8 @@ workflow GENEPAL {
         ch_benchmark_inputs.map { meta, gff, fasta, ref_gff -> [ meta, ref_gff ] }
     )
 
+    ch_multiqc_files            = ch_multiqc_files
+                                | mix(BENCHMARK.out.stats)
     ch_versions                 = ch_versions.mix(BENCHMARK.out.versions.first())
 
     // Collate and save software versions