TORCH-Consortium · Mxrcon · Aug 29, 2024 · Aug 29, 2024 · Sep 5, 2024
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -0,0 +1,37 @@
+report_comment: >
+  This report has been generated by the <a href="https://github.com/TORCH-Consortium/MAGMA" target="_blank">TORCH-Consortium/MAGMA</a>
+  analysis pipeline.
+
+export_plots: false
+
+disable_version_detection: true
+
+## Module order
+top_modules:
+  - "fastqc"
+  - custom_content
+
+
+custom_data:
+  cohort_qc:
+    section_name: 'Cohort Quality control'
+    plot_type: 'table'
+    id: 'cohort_qc'
+    pconfig:
+      id: 'cohort_qc'
+      namespace: "Cohort Quality Control"
+
+  distance_matrix:
+    section_name: "SNP Distance Matrix"
+    plot_type: 'heatmap'
+    id: 'distance_matrix'
+    pconfig:
+      id: 'distance_matrix'
+      max: 30
+      min: 0
+      tt_decimals: 0
+sp:
+  cohort_qc:
+    fn: "joint.merged_cohort_stats.tsv"
+  distance_matrix:
+    fn: "joint.ExDR.ExComplex.snp_dists.tsv"
diff --git a/main.nf b/main.nf
@@ -93,8 +93,10 @@ workflow {
                         UTILS_MERGE_COHORT_STATS.out.merged_cohort_stats_ch,
                         MERGE_WF.out.major_variants_results_ch,
                         MINOR_VARIANTS_ANALYSIS_WF.out.minor_variants_results_ch,
-                        STRUCTURAL_VARIANTS_ANALYSIS_WF.out.structural_variants_results_ch )
-
+                        STRUCTURAL_VARIANTS_ANALYSIS_WF.out.structural_variants_results_ch, 
+			MERGE_WF.out.snps_dists_ch
+			)
+
         }
     }
 }
diff --git a/modules/multiqc/multiqc.nf b/modules/multiqc/multiqc.nf
@@ -3,16 +3,23 @@ process MULTIQC {
     label 'cpu_4_memory_16'
 
     input:
+    	path(multiqc_config)
         path("*")
 
     output:
         tuple path("multiqc_data"), path("multiqc_report.html")
 
 
     script:
+        def config = multiqc_config ? "--config $multiqc_config" : ''
+
+        //FIXME @davi
+        def process_inputs = '' // !params.skip_merge_analysis ? 'preprocess.py --param 1 --param 2' : ''
 
         """
-        ${params.multiqc_path} .
+        ${process_inputs} 
+
+        ${params.multiqc_path} $config .
         """
 
     stub:

diff --git a/modules/snpdists/snpdists.nf b/modules/snpdists/snpdists.nf
@@ -8,6 +8,7 @@ process SNPDISTS {
 
     output:
         tuple val(joint_name), path("*.snp_dists.tsv")
+	path("*snp_dists.tsv"), emit: snp_dists_file 
 
     script:
 

diff --git a/workflows/merge_wf.nf b/workflows/merge_wf.nf
@@ -119,6 +119,5 @@ workflow MERGE_WF {
 
     emit:
         major_variants_results_ch =  MAJOR_VARIANT_ANALYSIS.out.major_variants_results_ch
-
-
+	snps_dists_ch = PHYLOGENY_ANALYSIS__EXCOMPLEX.out.snp_dists_ch
 }
diff --git a/workflows/reports_wf.nf b/workflows/reports_wf.nf
@@ -12,11 +12,13 @@ workflow REPORTS_WF {
          major_variants_results_ch
          minor_variants_results_ch
          structural_variants_results_ch
+	 snp_distances_ch
 
     main:
-        MULTIQC(reports_fastqc_ch)
+
+	ch_multiqc_files = Channel.empty()
 
-        UTILS_SUMMARIZE_RESISTANCE_RESULTS(
+	UTILS_SUMMARIZE_RESISTANCE_RESULTS(
             merged_cohort_stats_ch,
             major_variants_results_ch,
             minor_variants_results_ch,
@@ -28,6 +30,14 @@ workflow REPORTS_WF {
             minor_variants_results_ch,
             structural_variants_results_ch
         )
+        ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
 
+        ch_multiqc_files = ch_multiqc_files.mix(
+	reports_fastqc_ch,
+	merged_cohort_stats_ch,
+	snp_distances_ch
+	)
 
+        MULTIQC(ch_multiqc_config,
+	ch_multiqc_files.collect())
 }
diff --git a/workflows/subworkflows/phylogeny_analysis.nf b/workflows/subworkflows/phylogeny_analysis.nf
@@ -63,5 +63,5 @@ workflow PHYLOGENY_ANALYSIS {
 
     emit:
         snpsites_tree_tuple = SNPSITES.out.join(IQTREE.out.tree_tuple)
-
+	snp_dists_ch = SNPDISTS.out.snp_dists_file
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,7 @@ process SNPDISTS { @@
         output:
             tuple val(joint_name), path("*.snp_dists.tsv")
+    	path("*snp_dists.tsv"), emit: snp_dists_file
         script:
@@ Expand Down @@