Fixed multiqc config for busco

Plant-Food-Research-Open · Oct 8, 2024 · 8d348df · 8d348df
1 parent 6e117b1
commit 8d348df
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Showing 4 changed files with 27 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+1. Added MultiQC [#65](https://github.com/plant-food-research-open/genepal/issues/65)
+
 ### `Fixed`
 
 ### `Dependencies`
@@ -41,8 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 22. Added `benchmark` column to the input sheet and used `GFFCOMPARE` to perform benchmarking [#63](https://github.com/plant-food-research-open/genepal/issues/63)
 23. Added `SEQKIT_RMDUP` to detect duplicate sequence and wrap the fasta to 80 characters
 24. Updated parameter section labels for annotation and post-annotation filtering [#64](https://github.com/plant-food-research-open/genepal/issues/64)
-25. Added MultiQC [#65](https://github.com/plant-food-research-open/genepal/issues/65)
-26. Updated modules and sub-workflows
+25. Updated modules and sub-workflows
 
 ### `Fixed`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -2,16 +2,14 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/plant-food-research-open/genepal" target="_blank">plant-food-research-open/genepal</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://github.com/plant-food-research-open/genepal/blob/dev/docs/usage.md" target="_blank">documentation</a>.
+
 report_section_order:
   "plant-food-research-open-genepal-methods-description":
     order: -1000
-  software_versions:
-    order: -1001
   "plant-food-research-open-genepal-summary":
-    order: -1002
-
-export_plots: true
+    order: -1001
 
+export_plots: false
 disable_version_detection: true
 
 module_order:
@@ -26,3 +24,13 @@ module_order:
       info: "This section of the report shows FastQC results after adapter trimming."
       path_filters:
         - "*_trim*fastqc.zip"
+  - busco:
+      name: "BUSCO"
+      info: "Genome completeness statistics"
+      path_filters:
+        - "*seqkit.rmdup.fasta.txt"
+  - busco:
+      name: "BUSCO Annotation"
+      info: "Annotation completeness statistics"
+      path_filters_exclude:
+        - "*seqkit.rmdup.fasta.txt"
diff --git a/conf/modules.config b/conf/modules.config
@@ -383,10 +383,12 @@ process { // Universal
     }
 
     withName: MULTIQC {
+        ext.args = '--verbose'
         publishDir = [
-            path: { "${params.outdir}/multiqc" },
+            path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            pattern: 'multiqc_report.html'
         ]
     }
 }
diff --git a/workflows/genepal.nf b/workflows/genepal.nf
@@ -220,6 +220,9 @@ workflow GENEPAL {
         [] // val_busco_config
     )
 
+    ch_multiqc_files            = ch_multiqc_files
+                                | mix(FASTA_GXF_BUSCO_PLOT.out.assembly_short_summaries_txt)
+                                | mix(FASTA_GXF_BUSCO_PLOT.out.annotation_short_summaries_txt)
     ch_versions                 = ch_versions.mix(FASTA_GXF_BUSCO_PLOT.out.versions)
 
     // SUBWORKFLOW: GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES
@@ -276,7 +279,10 @@ workflow GENEPAL {
                                 | mix(ch_methods_description)
 
     MULTIQC (
-        ch_multiqc_files.map { meta, file -> file }.mix(ch_multiqc_extra_files).collect(),
+        ch_multiqc_files
+        | map { meta, file -> file }
+        | mix(ch_multiqc_extra_files)
+        | collect,
         ch_multiqc_config.toList(),
         [],
         [],