Remove output files from all_outputs list that do not exist anymore

NBISweden · Oct 9, 2023 · 4c49098 · 4c49098
1 parent 92f7aa9
commit 4c49098
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diff --git a/workflow/rules/12_snpEff.smk b/workflow/rules/12_snpEff.smk
@@ -4,23 +4,19 @@
 
 # Code collecting output files from this part of the pipeline
 if os.path.exists(config["historical_samples"]) and os.path.exists(config["modern_samples"]):
-    all_outputs.append(expand("results/{dataset}/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html",
-        dataset=["historical", "modern"]))
     all_outputs.append(expand("results/all/snpEff/" + REF_NAME + ".all.fmissing{fmiss}.{chr}.snpEff_variant_impact_plot.pdf", 
         fmiss=config["f_missing"],
         chr=CHR,))
     all_outputs.append("results/historical/snpEff/" + REF_NAME + "/multiqc/multiqc_report.html")
     all_outputs.append("results/modern/snpEff/" + REF_NAME + "/multiqc/multiqc_report.html")
 
 elif os.path.exists(config["historical_samples"]):
-    all_outputs.append("results/historical/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html")
     all_outputs.append(expand("results/historical/snpEff/" + REF_NAME + ".historical.fmissing{fmiss}.{chr}.snpEff_variant_impact_plot.pdf",
         fmiss=config["f_missing"],
         chr=CHR,))
     all_outputs.append("results/historical/snpEff/" + REF_NAME + "/multiqc/multiqc_report.html")
 
 elif os.path.exists(config["modern_samples"]):
-    all_outputs.append("results/modern/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html")
     all_outputs.append(expand("results/modern/snpEff/" + REF_NAME + ".modern.fmissing{fmiss}.{chr}.snpEff_variant_impact_plot.pdf",
         fmiss=config["f_missing"],
         chr=CHR,))

diff --git a/workflow/rules/13_GERP.smk b/workflow/rules/13_GERP.smk
@@ -7,24 +7,20 @@ all_outputs.append(expand("results/gerp/" + REF_NAME + ".{chr}.ancestral.rates.g
     chr=CHR,))
 
 if os.path.exists(config["historical_samples"]) and os.path.exists(config["modern_samples"]):
-    all_outputs.append(expand("results/{dataset}/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html",
-        dataset=["historical", "modern"]))
     all_outputs.append(expand("results/gerp/all/" + REF_NAME + ".all.fmissing{fmiss}.{chr}.relative_mutational_load.gerp_{minGERP}_{maxGERP}_plot.pdf",
             fmiss=config["f_missing"],
             chr=CHR,
             minGERP=config["min_gerp"],
             maxGERP=config["max_gerp"],))
 
 elif os.path.exists(config["historical_samples"]):
-    all_outputs.append("results/historical/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html")
     all_outputs.append(expand("results/gerp/historical/" + REF_NAME + ".historical.fmissing{fmiss}.{chr}.relative_mutational_load.gerp_{minGERP}_{maxGERP}_plot.pdf",
             fmiss=config["f_missing"],
             chr=CHR,
             minGERP=config["min_gerp"],
             maxGERP=config["max_gerp"],))
 
 elif os.path.exists(config["modern_samples"]):
-    all_outputs.append("results/modern/vcf/" + REF_NAME + "/stats/multiqc/multiqc_report.html")
     all_outputs.append(expand("results/gerp/modern/" + REF_NAME + ".modern.fmissing{fmiss}.{chr}.relative_mutational_load.gerp_{minGERP}_{maxGERP}_plot.pdf",
             fmiss=config["f_missing"],
             chr=CHR,