Merge branch 'add_lineage' of https://github.com/jts/ncov-tools into …

…watch

workflow/Snakefile

@@ -13,4 +13,5 @@ rule all:
     input:
         get_qc_sequencing_plots,
         get_qc_analysis_plots,
-        get_qc_reports
+        get_qc_reports,
+        get_recurrent_heatmap_plot

workflow/rules/analysis.smk

@@ -142,7 +142,10 @@ rule make_sample_qc_summary:
         alleles=get_run_alleles,
         samplecoverage="qc_sequencing/{sample}.per_base_coverage.bed",
         samplevariants=get_variants,
-        sampleconsensus=get_consensus
+        sampleconsensus=get_consensus,
+        lineagereport=get_lineage_report,
+        aa_table="qc_annotation/{sample}_aa_table.tsv",
+        watch=get_watch_variants_report
     output:
         "qc_analysis/{sample}.summary.qc.tsv"
     params:
@@ -157,6 +160,9 @@ rule make_sample_qc_summary:
                             --indel \
                             --consensus {input.sampleconsensus} {params.platform_opt} \
                             --sample {wildcards.sample} \
+                            --lineage {input.lineagereport} \
+                            --aa_table {input.aa_table} \
+                            --mutations {input.watch} \
                             --run_name {params.run_name_opt} > {output}"
 
 # merge the per-sample summary files into the run-level report

workflow/rules/common.smk

@@ -95,12 +95,17 @@ def get_tree_consensus_sequences(wildcards):
     return consensus_sequences
 
 def get_tree_plot_input(wildcards):
-
-    input_list = ["qc_analysis/{prefix}_tree.nwk", "qc_analysis/{prefix}_alleles.tsv"]
-    if "assign_lineages" in config and config["assign_lineages"]:
-        input_list.append("lineages/{prefix}_lineage_report.csv")
+    input_list = ["qc_analysis/{prefix}_tree.nwk", "qc_analysis/{prefix}_alleles.tsv", "lineages/{prefix}_lineage_report.csv"]
     return input_list
 
+def get_lineage_report(wildcards):
+    lineage_report = f"lineages/{config['run_name']}_lineage_report.csv"
+    return lineage_report
+
+def get_watch_variants_report(wildcards):
+    watch_variants_report = f"qc_reports/{config['run_name']}_ncov_watch_variants.tsv"
+    return watch_variants_report
+
 def get_qc_sequencing_plots(wildcards):
     prefix = get_run_name()
     out = [ "plots/%s_amplicon_covered_fraction.pdf" % (prefix),