successfully run old coloc including NULL hypothesis #29

ht-diva · Dec 10, 2024 · 1553edf · 1553edf
1 parent 88daa42
commit 1553edf
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diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -26,4 +26,4 @@ rule all:
         ws_path("break/collected_loci_excluding_mhc.csv"),
         ws_path("cojo/collected_credible_sets.csv"),
         expand(ws_path("coloc/{seqid}_master_file.sentinel"), seqid=analytes.seqid),
-        expand(ws_path("coloc/chr{chr_cs}.sentinel"), chr_cs = range(19, 20))
+        expand(ws_path("coloc/chr{chr_cs}_colocalization.table.all.tsv"), chr_cs = range(19,20)),
diff --git a/workflow/rules/coloc.smk b/workflow/rules/coloc.smk
@@ -40,3 +40,24 @@ rule merry_go_round:
         
         touch {output.sentinel}
         """
+
+
+rule run_coloc:
+    input:
+        sentinel = ws_path("coloc/chr{chr_cs}.sentinel"),
+    output:
+        ofile = ws_path("coloc/chr{chr_cs}_colocalization.table.all.tsv"),
+    conda:
+        "../envs/fine_mapping.yml"
+    params:
+        codes = config.get("path_code"),
+        pairs = ws_path("coloc/chr{chr_cs}_coloc_pairwise_guide_table.tsv"),
+        chr = "{chr_cs}",
+    shell:
+        """
+        Rscript workflow/scripts/s06_coloc.R \
+            --pipeline_path {params.codes} \
+            --coloc_guide_table {params.pairs} \
+            --chr_cs {params.chr}  \
+            --ofile {output.ofile}
+        """