diff --git a/workflow/Snakefile b/workflow/Snakefile index 7370ba7..4291d80 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -86,7 +86,7 @@ rule all: expand(join(workpath, config['project']['id'], "metawrap_binning", "{name}", "figures", "binning_results.png"), name=samples), # bin refinement # ~~~~~~~~~~~~~~~ - expand(join(top_refine_dir, "{name}", "dereplicated_bins"), name=samples), + expand(join(top_refine_dir, "{name}", "{name}_dREP_COMPLETE"), name=samples), join(top_refine_dir, "RefinedBins_summmary.txt"), join(top_refine_dir, "cumulative_stats_maxbin.txt"), join(top_refine_dir, "cumulative_stats_metabat2.txt"), diff --git a/workflow/rules/DNA.smk b/workflow/rules/DNA.smk index 9d13dbd..5672eef 100644 --- a/workflow/rules/DNA.smk +++ b/workflow/rules/DNA.smk @@ -504,6 +504,7 @@ rule derep_bins: bin_breadcrumb = join(top_binning_dir, "{name}", "{name}_BINNING_COMPLETE"), output: dereplicated_bins = directory(join(top_refine_dir, "{name}", "dereplicated_bins")), + deprep_bc = join(top_refine_dir, "{name}", "{name}_dREP_COMPLETE"), singularity: metawrap_container, threads: int(cluster["derep_bins"].get("threads", default_threads)), params: @@ -532,4 +533,5 @@ rule derep_bins: -nc {params.min_overlap} \ -cm {params.coverage_method} \ {output.dereplicated_bins} + touch {output.deprep_bc} """