feat: FLiRT Mutations column (#664)

* init

* fmt

* add to other config.yaml and template files

* add def

* add to env output

* fmt

.tests/config/config.yaml

@@ -166,6 +166,12 @@ mixtures:
     - "_MIX_B-1-1-7_PERC_90_MIX_B-1-351_PERC_10"
 
 # mutations to be highlighted (protein name -> variants)
+
+flirt:
+  S:
+    - F456L
+    - R346T
+
 mth:
   S:
     - N501Y

config/config.yaml

@@ -21,7 +21,7 @@ data-handling:
   # flag for archiving data
   # True: data is archived in path defined below
   # False: data is not archived
-  archive-data: True
+  archive-data: False
   # path of incoming data, which is moved to the
   # data directory by the preprocessing script
   incoming: ../incoming/
@@ -34,7 +34,7 @@ data-handling:
 quality-criteria:
   illumina:
     # minimal length of acceptable reads
-    min-length-reads: 30
+    min-length-reads: 100
     # average quality of acceptable reads (PHRED)
     min-PHRED: 20
   ont:
@@ -61,9 +61,9 @@ preprocessing:
   # ARTIC primer version to clip from reads. See
   # https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4
   # for more information
-  artic-primer-version: 3
+  artic-primer-version: 4
   # path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
-  amplicon-primers: "resources/nCoV-2019.primer.bed"
+  amplicon-primers: "resources/SARS-CoV-2-artic-v4_1.primer.bed"
   # GenBank accession of reference sequence of the amplicon primers
   amplicon-reference: "MN908947"
 
@@ -124,6 +124,12 @@ strain-calling:
     B.1.617.2: OK091006
 
 # mutations to be highlighted (protein name -> variants)
+
+flirt:
+  S:
+    - F456L
+    - R346T
+
 mth:
   S:
     - L18F

resources/report-table-formatter.js

@@ -91,6 +91,9 @@
       }
 
   },
+  "FLiRT Mutations": function format(value) {
+    return this["variant helper"](value, true);
+  },
   "VOC Mutations": function format(value) {
       return this["variant helper"](value, true);
   },

workflow/rules/generate_output.smk

@@ -153,6 +153,7 @@ rule overview_table_patient_csv:
             wildcards, "all samples"
         ),
         mth=config.get("mth"),
+        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -178,6 +179,7 @@ use rule overview_table_patient_csv as overview_table_environment_csv with:
         qc_data="results/{date}/tables/environment-overview.csv",
     params:
         mth=config.get("mth"),
+        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -371,6 +373,7 @@ rule snakemake_reports_patient:
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
         ),
+        # lambda wildcards: "results/{date}/lineage-variant-report/all",
         lambda wildcards: expand(
             "results/{{date}}/vcf-report/{target}.{filter}.{annotation}",
             target=get_samples_for_date(wildcards.date) + ["all"],
@@ -380,10 +383,10 @@ rule snakemake_reports_patient:
         # 3. Sequencing Details
         "results/{date}/qc/laboratory/multiqc.html",
         "results/{date}/plots/coverage-reference-genome.png",
-        "results/{date}/plots/coverage-assembled-genome.png",
-        lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
-        if any_sample_is_amplicon(wildcards)
-        else [],
+        # "results/{date}/plots/coverage-assembled-genome.png",
+        # lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
+        # if any_sample_is_amplicon(wildcards)
+        # else [],
         # 4. Assembly
         "results/{date}/filter-overview",
         "results/{date}/pangolin-call-overview",
@@ -406,8 +409,6 @@ rule snakemake_reports_patient:
         "results/patient-reports/{date}.zip",
     params:
         for_testing=get_if_testing("--snakefile ../workflow/Snakefile"),
-    conda:
-        "../envs/snakemake.yaml"
     log:
         "logs/snakemake_reports/{date}.log",
     shell:
@@ -423,10 +424,10 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
             "results/{{date}}/{execution_mode}/overview/",
             execution_mode=get_checked_mode(),
         ),
-        "results/{date}/plots/all.major-strain.strains.kallisto.svg",
-        expand_samples_for_date(
-            ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
-        ),
+        # "results/{date}/plots/all.major-strain.strains.kallisto.svg",
+        # expand_samples_for_date(
+        #     ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
+        # ),
         # 2. Variant Call Details
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
@@ -444,3 +445,8 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
         "results/environment-reports/{date}.zip",
     log:
         "logs/snakemake_reports/{date}.log",
+
+
+# rule output_sample_sheet:
+#     input:
+#         Path(pep.config_file()).parent / pep.config()["sample_table"],

workflow/schemas/config.schema.yaml

@@ -115,6 +115,9 @@ properties:
         description: flag for using gisaid or genbank
       lineage-references:
         type: object
+  flirt:
+    type: object
+    description: mutations to be highlighted (protein name -> variants)
   mth:
     type: object
     description: mutations to be highlighted (protein name -> variants)
@@ -130,4 +133,5 @@ required:
   - assembly
   - variant-calling
   - strain-calling
+  - flirt
   - mth

workflow/scripts/generate-overview-table.py

@@ -193,6 +193,7 @@ def register_contig_lengths(assemblies, name):
 }
 
 for sample, file in iter_with_samples(snakemake.input.bcf):
+    flirt_mutations = {}
     mutations_of_interest = {}
     other_mutations = {}
 
@@ -228,11 +229,14 @@ def fmt_variants(variants):
 
                     hgvsp = f"{feature}:{alteration}"
                     entry = (hgvsp, f"{vaf:.3f}")
-                    if alteration in snakemake.params.mth.get(feature, {}):
+                    if alteration in snakemake.params.flirt.get(feature, {}):
+                        insert_entry(flirt_mutations, hgvsp, vaf)
+                    elif alteration in snakemake.params.mth.get(feature, {}):
                         insert_entry(mutations_of_interest, hgvsp, vaf)
                     else:
                         insert_entry(other_mutations, hgvsp, vaf)
 
+    data.loc[sample, "FLiRT Mutations"] = fmt_variants(flirt_mutations)
     data.loc[sample, "VOC Mutations"] = fmt_variants(mutations_of_interest)
     data.loc[sample, "Other Mutations"] = fmt_variants(other_mutations)