Add a conditional output if there is no results

akcorut · Nov 22, 2021 · 51798c8 · 51798c8
1 parent df236ed
commit 51798c8
Showing 1 changed file with 9 additions and 4 deletions.
diff --git a/workflow/rules/fetch_kmers.smk b/workflow/rules/fetch_kmers.smk
@@ -9,15 +9,20 @@ checkpoint fetch_kmers_from_res_table:
     output:
         directory("results/fetch_kmers")
     params:
-        threshold = config["params"]["fetch_kmers"]["threshold"]
+        threshold = config["params"]["fetch_kmers"]["threshold"],
+        check_file = "results/kmers_gwas_summary/NO_KMERS_PASS_5PER_THRESHOLD_FOUND"
     conda:
         "../envs/kmers_stats.yaml"
     message:
         "Fetching significant k-mers for each phenotype from kmersGWAS results table ({input.res_tab})..."
     shell:
-        """
-        python scripts/fetch_kmers_from_results_table.py -i {input.res_tab} \
-        -t {params.threshold} -p {input.phenos_list} -o {output}
+        r"""
+        if [ -f {params.check_file} ]; then
+            mkdir {output} # Do nothing : Just create empty folder
+        else
+            python scripts/fetch_kmers_from_results_table.py -i {input.res_tab} \
+            -t {params.threshold} -p {input.phenos_list} -o {output}
+        fi
         """
 
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