implementation of multiqc report generation for the V1 report

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
+			)
+
         }
     }
 }

modules/multiqc/multiqc.nf

@@ -3,16 +3,18 @@ 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" : ''
 
         """
-        ${params.multiqc_path} .
+        ${params.multiqc_path} $config .
         """
 
     stub:

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:
 

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
 }

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())
 }

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
 }