feat: added variants-over-time-plot to report again (#405)

* Added variant-plots-over-time to report * fmt * Correction of code in snakemake_reports * fmt Co-authored-by: Thomas Battenfeld <[email protected]>
IKIM-Essen · Dec 15, 2021 · bd5048a · bd5048a
1 parent 74f3077
commit bd5048a
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Showing 6 changed files with 58 additions and 7 deletions.
diff --git a/workflow/rules/benchmarking.smk b/workflow/rules/benchmarking.smk
@@ -264,7 +264,9 @@ rule assembly_comparison_velvet:
 
 rule order_contigs_assembly_comparison:
     input:
-        contigs="results/{date}/assembly/{sample}/{assembler}-pe/{sample}.contigs.fasta",
+        contigs=(
+            "results/{date}/assembly/{sample}/{assembler}-pe/{sample}.contigs.fasta"
+        ),
         reference="resources/genomes/main.fasta",
     output:
         temp(

diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk
@@ -251,6 +251,39 @@ rule plot_lineages_over_time:
         "../scripts/plot-lineages-over-time.py"
 
 
+rule plot_variants_over_time:
+    input:
+        bcf=lambda wildcards: expand(
+            "results/{date}/filtered-calls/ref~main/{sample}.subclonal.high+moderate-impact.bcf",
+            zip,
+            date=get_dates_before_date(wildcards),
+            sample=get_samples_before_date(wildcards),
+        ),
+        csi=lambda wildcards: expand(
+            "results/{date}/filtered-calls/ref~main/{sample}.subclonal.high+moderate-impact.bcf.csi",
+            zip,
+            date=get_dates_before_date(wildcards),
+            sample=get_samples_before_date(wildcards),
+        ),
+    output:
+        report(
+            "results/{date}/plots/variants-{ORFNAME}-over-time.svg",
+            caption="../report/variants-over-time.rst",
+            category="1. Overview",
+            subcategory="3. Variants Development",
+        ),
+        "results/{date}/tables/variants-{ORFNAME}-over-time.csv",
+    params:
+        dates=get_dates_before_date,
+        samples=get_samples_before_date,
+    log:
+        "logs/{date}/{ORFNAME}-over-time.log",
+    conda:
+        "../envs/python.yaml"
+    script:
+        "../scripts/plot-variants-over-time.py"
+
+
 rule pangolin_call_overview_csv:
     input:
         get_aggregated_pangolin_calls,
@@ -297,6 +330,10 @@ rule snakemake_reports:
         # 1. Overview
         "results/{date}/overview/",
         "results/{date}/plots/lineages-over-time.svg",
+        expand(
+            "results/{{date}}/tables/variants-{ORFNAME}-over-time.csv",
+            ORFNAME=config["orf_names"],
+        ),
         "results/{date}/plots/all.strains.pangolin.svg",
         "results/{date}/plots/all.major-strain.strains.kallisto.svg",
         expand_samples_for_date(

diff --git a/workflow/rules/long_read.smk b/workflow/rules/long_read.smk
@@ -63,7 +63,9 @@ rule customize_primer_porechop:
 
 rule porechop_primer_trimming:
     input:
-        fastq_in="results/{date}/trimmed/porechop/adapter_barcode_trimming/{sample}.fastq",
+        fastq_in=(
+            "results/{date}/trimmed/porechop/adapter_barcode_trimming/{sample}.fastq"
+        ),
         repl_flag="results/.indicators/replacement_notice.txt",
     output:
         "results/{date}/trimmed/porechop/primer_clipped/{sample}.fastq",

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -41,7 +41,9 @@ rule multiqc:
         input_dirs=lambda w, input: set(path.dirname(fp) for fp in input),
         output_dir=lambda w, output: path.dirname(output[0]),
         output_name=lambda w, output: path.basename(output[0]),
-        params="--config config/multiqc_config.yaml --title 'Results for data from {date}'",
+        params=(
+            "--config config/multiqc_config.yaml --title 'Results for data from {date}'"
+        ),
     log:
         "logs/{date}/multiqc.log",
     conda:
@@ -134,7 +136,9 @@ rule species_diversity_before_pe:
         kraken_output=temp(
             "results/{date}/species-diversity/pe/{sample}/{sample}.kraken"
         ),
-        report="results/{date}/species-diversity/pe/{sample}/{sample}.uncleaned.kreport2",
+        report=(
+            "results/{date}/species-diversity/pe/{sample}/{sample}.uncleaned.kreport2"
+        ),
     log:
         "logs/{date}/kraken/pe/{sample}.log",
     params:
@@ -161,7 +165,9 @@ rule species_diversity_before_se:
         kraken_output=temp(
             "results/{date}/species-diversity/se/{sample}/{sample}.kraken"
         ),
-        report="results/{date}/species-diversity/se/{sample}/{sample}.uncleaned.kreport2",
+        report=(
+            "results/{date}/species-diversity/se/{sample}/{sample}.uncleaned.kreport2"
+        ),
     log:
         "logs/{date}/kraken/se/{sample}.log",
     threads: 8

diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
@@ -10,7 +10,9 @@ rule samtools_sort:
     output:
         "results/{date}/read-sorted/{read_type}~{sorted_by}/{sample}.{stage}.bam",
     params:
-        extra=lambda wildcards: "-n -m 4G" if wildcards.sorted_by == "name" else "-m 4G",
+        extra=(
+            lambda wildcards: "-n -m 4G" if wildcards.sorted_by == "name" else "-m 4G"
+        ),
         tmp_dir="/tmp/",
     log:
         "logs/{date}/sort-bam/{read_type}~{sorted_by}/{sample}.{stage}.log",

diff --git a/workflow/rules/variant_report.smk b/workflow/rules/variant_report.smk
@@ -43,7 +43,9 @@ rule ucsc_vcf:
         bcfs=get_report_input(
             "results/{date}/filtered-calls/ref~main/{sample}.subclonal.{filter}.bcf"
         ),
-        strain_call="results/{date}/tables/strain-calls/{target}.polished.strains.pangolin.csv",
+        strain_call=(
+            "results/{date}/tables/strain-calls/{target}.polished.strains.pangolin.csv"
+        ),
     output:
         report(
             "results/{date}/ucsc-vcfs/{target}.{filter}.vcf",