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sanjaynagi · Jun 26, 2024 · be212c2 · be212c2
1 parent d94e12f
commit be212c2
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Showing 4 changed files with 3 additions and 82 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -15,23 +15,14 @@ metadata = load_metadata(config['metadata'])
 validate(metadata, schema="schemas/samples.schema.yaml")
 samples = metadata["sampleID"]
 
-# AlleleBalance mutations file
-if config["miscellaneous"]["VariantsOfInterest"]["activate"]:
-    mutationData = pd.read_csv(
-        config["miscellaneous"]["VariantsOfInterest"]["path"], sep="\t"
-    )
-else:
-    mutationData = pd.DataFrame(
-        {"Name": ["KDR"], "mut": ["995F"], "Location": ["2L-28xxxxx"]}
-    )  # ignore this, just an dummy df for snakemake
-
-
+if config['miscellaneous']['VariantsOfInterest']['activate']:
+    mutationData =  pd.read_csv(config["miscellaneous"]["VariantsOfInterest"]["path"], sep="\t")
+    include: "rules/variantsOfInterest.smk"
 
 welcome(version="v2.0.2")
 
 include: "rules/qc.smk"
 include: "rules/diffexp.smk"
-include: "rules/variantsOfInterest.smk"
 include: "rules/alignment.smk"
 include: "rules/variantCalling.smk"
 include: "rules/filterAnnotate.smk"

diff --git a/workflow/rules/diffexp.smk b/workflow/rules/diffexp.smk
@@ -155,24 +155,6 @@ rule Ag1000gSweepsDE:
         "../scripts/Ag1000gSweepsDE.py"
 
 
-# rule geneFamilies:
-#     input:
-#         genediff=expand("results/genediff/{comp}.csv", comp=config["contrasts"]),
-#         normcounts="results/counts/normCounts.tsv",
-#         eggnog=config["miscellaneous"]["GeneFamiliesHeatmap"]["eggnog"],
-#         pfam=config["miscellaneous"]["GeneFamiliesHeatmap"]["pfam"],
-#     output:
-#         heatmaps="results/genediff/GeneFamiliesHeatmap.pdf",
-#     conda:
-#         "../envs/pythonGenomics.yaml"
-#     log:
-#         "logs/geneFamilies.log",
-#     params:
-#         DEcontrasts=config["contrasts"],
-#     script:
-#         "../scripts/GeneFamiliesHeatmap.py"
-
-
 rule geneFamilies_notebook:
     """
     Summarise gene expression for gene families

diff --git a/workflow/rules/variantAnalysis.smk b/workflow/rules/variantAnalysis.smk
@@ -35,37 +35,6 @@ rule SNPstatistics:
     script:
         "../scripts/SNPstatistics.py"
 
-# rule PCA:
-#     """
-#     Perform pca on genotype data and plot 
-#     """
-#     input:
-#         vcf=expand(
-#             "results/variantAnalysis/vcfs/{dataset}.{contig}.vcf.gz",
-#             contig=config["contigs"],
-#             dataset=config["dataset"],
-#         ),
-#         metadata=config["metadata"],
-#     output:
-#         PCAfig=expand(
-#             "results/variantAnalysis/pca/PCA-{contig}-{dataset}.svg",
-#             contig=config["contigs"],
-#             dataset=config["dataset"],
-#         ),
-#     log:
-#         "logs/pca.log",
-#     conda:
-#         "../envs/pythonGenomics.yaml"
-#     params:
-#         dataset=config["dataset"],
-#         contigs=config["contigs"],
-#         ploidy=config["VariantAnalysis"]["ploidy"],
-#         missingprop=config["VariantAnalysis"]["pca"]["missingness"],
-#         qualflt=30,
-#     script:
-#         "../scripts/pca.py"
-
-
 rule pca_notebook:
     """
     Perform pca on genotype data and plot 

diff --git a/workflow/rules/variantsOfInterest.smk b/workflow/rules/variantsOfInterest.smk
@@ -53,27 +53,6 @@ rule AlleleBalanceVariantsOfInterest:
         "../scripts/VariantsOfInterestAlleleBalance.R"
 
 
-# rule PlotVariantsOfInterest:
-#     """
-#     Python script to plot frequencies of Variants of interest
-#     """
-#     input:
-#         expand(
-#             "results/variantAnalysis/variantsOfInterest/csvs/{mut}_alleleBalance.csv",
-#             mut=mutationData.Name,
-#         ),
-#         VariantsOfInterest=config["miscellaneous"]["VariantsOfInterest"]["path"],
-#     output:
-#         perSampleHeatmap="results/variantAnalysis/variantsOfInterest/VOI.heatmapPerSample.svg",
-#         perTreatmentHeatmap="results/variantAnalysis/variantsOfInterest/VOI.heatmapPerTreatment.svg",
-#     conda:
-#         "../envs/pythonGenomics.yaml"
-#     priority: 10
-#     log:
-#         "logs/variantsOfInterestPlot.log",
-#     script:
-#         "../scripts/VariantsOfInterestPlot.py"
-
 
 rule VariantsOfInterest_notebook:
     """