add the new process to the workflow and the datatable

bin/summary_report.py

@@ -640,6 +640,9 @@ def unclass_markup(value):
 
         self.add_col_description(f'Read classification was determined against a database containing only SARS-CoV-2 and human with <a href="https://ccb.jhu.edu/software/kraken2/">Kraken2</a> (v{self.tool_versions["kraken2"]}).')
 
+    def add_mixed_sites_results(self, mixed_site_results):
+        res_data = pd.read_csv(mixed_site_results, index_col='sample', dtype={'sample': str})
+        self.add_column_raw('num_mixed_sites', res_data['num_mixed_sites'])
 
     def add_coverage_plots(self, coverage_plots):
         for coverage_plot in sorted(coverage_plots.split(',')):
@@ -826,6 +829,7 @@ def get_lineage_status(self, lineage):
     parser.add_argument("-n", "--nextclade_results", help="nextclade results")
     parser.add_argument("-q", "--president_results", help="president results")
     parser.add_argument("-k", "--kraken2_results", help="kraken2 results")
+    parser.add_argument("-m", "--mixed_sites_results", help="mixed sites statisics")
     parser.add_argument("-c", "--coverage_plots", help="coverage plots (comma separated)")
     parser.add_argument("-s", "--samples", help="sample ids (comma separated)")
     args = parser.parse_args()
@@ -852,6 +856,8 @@ def get_lineage_status(self, lineage):
         report.add_pangolin_results(args.pangolin_results)
     if args.nextclade_results:
         report.add_nextclade_results(args.nextclade_results)
+    if args.mixed_sites_results:
+        report.add_mixed_sites_results(args.mixed_sites_results)
     if args.coverage_plots:
         report.add_coverage_plots(args.coverage_plots)
 

poreCov.nf

@@ -309,6 +309,7 @@ include { get_fasta } from './modules/get_fasta_test_data.nf'
 include { align_to_reference } from './modules/align_to_reference.nf'
 include { split_fasta } from './modules/split_fasta.nf'
 include { filter_fastq_by_length } from './modules/filter_fastq_by_length.nf'
+include { add_alt_allele_ration_vcf } from './modules/add_alt_allele_ration_vcf.nf'
 
 /************************** 
 * Workflows
@@ -405,6 +406,15 @@ workflow {
         determine_mutations_wf(fasta_input_ch)
         genome_quality_wf(fasta_input_ch, reference_for_qc_input_ch)
 
+        // add alternative allele ratio to the VCF
+        if (params.primerV.toString().contains(".bed")) {
+            external_primer_schemes = artic_ncov_wf.out.primer_dir
+        }
+        else {
+            external_primer_schemes = file(workflow.projectDir + "/data/external_primer_schemes", checkIfExists: true, type: 'dir' )
+        }
+        add_alt_allele_ration_vcf(artic_ncov_wf.out.trimmed_bam.join(artic_ncov_wf.out.vcf).join(artic_ncov_wf.out.failed_vcf), external_primer_schemes)
+
     // 3. Specialised outputs (rki, json)
         rki_report_wf(genome_quality_wf.out[0], genome_quality_wf.out[1], extended_input_ch)
 
@@ -436,7 +446,7 @@ workflow {
         else { samples_table_ch = Channel.from( ['deactivated'] ) }
 */
         create_summary_report_wf(determine_lineage_wf.out, genome_quality_wf.out[0], determine_mutations_wf.out,
-                                taxonomic_read_classification_ch, alignments_ch, samples_file_ch)
+                                taxonomic_read_classification_ch, add_alt_allele_ration_vcf.out.stats, alignments_ch, samples_file_ch)
 
 }
 

workflows/create_summary_report.nf

@@ -8,6 +8,7 @@ workflow create_summary_report_wf {
         president
         nextclade
         kraken2
+        mixed_sites
         alignments
         samples_table
 
@@ -18,6 +19,7 @@ workflow create_summary_report_wf {
         pangolin_results = pangolin.map {it -> it[1]}.collectFile(name: 'pangolin_results.csv', skip: 1, keepHeader: true)
         president_results = president.map {it -> it[1]}.collectFile(name: 'president_results.tsv', skip: 1, keepHeader: true)
         nextclade_results = nextclade.map {it -> it[1]}.collectFile(name: 'nextclade_results.tsv', skip: 1, keepHeader: true)
+        mixed_site_results = mixed_sites.map {it -> it[1]}.collectFile(name: 'mixed_sites_results.tsv', skip: 1, keepHeader: true)
 
         alignment_files = alignments.map {it -> it[0]}.collect()
         if (params.fasta || workflow.profile.contains('test_fasta')) {
@@ -30,7 +32,7 @@ workflow create_summary_report_wf {
             coverage_plots = plot_coverages(alignments.map{it -> it[0]}.toSortedList({ a, b -> a.simpleName <=> b.simpleName }).flatten().collate(6), \
                                             alignments.map{it -> it[1]}.toSortedList({ a, b -> a.simpleName <=> b.simpleName }).flatten().collate(6)).collect()
 
-            if (params.samples) { summary_report(version_ch, variants_table_ch, pangolin_results, president_results, nextclade_results, kraken2_results, coverage_plots, samples_table) }
-            else { summary_report_default(version_ch, variants_table_ch, pangolin_results, president_results, nextclade_results, kraken2_results, coverage_plots) }
+            if (params.samples) { summary_report(version_ch, variants_table_ch, pangolin_results, president_results, nextclade_results, kraken2_results, mixed_site_results, coverage_plots, samples_table) }
+            else { summary_report_default(version_ch, variants_table_ch, pangolin_results, president_results, nextclade_results, kraken2_results, mixed_site_results, coverage_plots) }
         }
 } 

workflows/process/summary_report.nf

@@ -10,6 +10,7 @@ process summary_report {
         path(president_results)
         path(nextclade_results)
         file(kraken2_results)
+        file(mixed_sites_results)
         file(coverage_plots)
         file(samples_table)
     output:
@@ -43,6 +44,7 @@ process summary_report {
             -q !{president_results} \
             -n !{nextclade_results} \
             -k kraken2_results.csv \
+            -m !{mixed_sites_results} \
             -c $(echo !{coverage_plots} | tr ' ' ',') \
             -s !{samples_table}
         '''
@@ -64,6 +66,7 @@ process summary_report_default {
         path(president_results)
         path(nextclade_results)
         path(kraken2_results)
+        path(mixed_sites_results)
         path(coverage_plots)
     output:
 	    path("poreCov_summary_report_*.html")
@@ -96,6 +99,7 @@ process summary_report_default {
             -q !{president_results} \
             -n !{nextclade_results} \
             -k kraken2_results.csv \
+            -m !{mixed_sites_results} \
             -c $(echo !{coverage_plots} | tr ' ' ',') 
         '''
     stub: