From 4c490984fc31ce8990151b72892e0cad19e939af Mon Sep 17 00:00:00 2001 From: verku Date: Mon, 9 Oct 2023 11:39:02 +0200 Subject: [PATCH] Remove output files from all_outputs list that do not exist anymore --- workflow/rules/12_snpEff.smk | 4 ---- workflow/rules/13_GERP.smk | 4 ---- 2 files changed, 8 deletions(-) diff --git a/workflow/rules/12_snpEff.smk b/workflow/rules/12_snpEff.smk index 38ee804..6fd74b5 100644 --- a/workflow/rules/12_snpEff.smk +++ b/workflow/rules/12_snpEff.smk @@ -4,8 +4,6 @@ # 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,)) @@ -13,14 +11,12 @@ if os.path.exists(config["historical_samples"]) and os.path.exists(config["moder 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 index 42ae458..78d2afc 100644 --- a/workflow/rules/13_GERP.smk +++ b/workflow/rules/13_GERP.smk @@ -7,8 +7,6 @@ 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, @@ -16,7 +14,6 @@ if os.path.exists(config["historical_samples"]) and os.path.exists(config["moder 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, @@ -24,7 +21,6 @@ elif os.path.exists(config["historical_samples"]): 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,