fix: trigger and end dRep with breadcrumb

OpenOmics · Mar 1, 2024 · 8370422 · 8370422
1 parent a210cda
commit 8370422
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git 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
@@ -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}
         """