adding rule to combine coloc info tables #29

workflow/Snakefile

@@ -16,6 +16,7 @@ configfile: "conf/config_finemap.yaml"
 include: "rules/common.smk"
 include: "rules/locus_breaker.smk"
 include: "rules/cojo.smk"
+include: "rules/coloc.smk"
 
 
 rule all:
@@ -24,3 +25,4 @@ rule all:
         expand(ws_path("break/{seqid}_loci.csv"), seqid=analytes.seqid),
         ws_path("break/collected_loci_excluding_mhc.csv"),
         ws_path("cojo/collected_credible_sets.csv"),
+        ws_path("coloc/master_coloc.txt"),

workflow/rules/coloc.smk

@@ -0,0 +1,17 @@
+
+rule make_file:
+    input:
+        expand(ws_path("cojo/{seqid}.sentinel"), seqid=analytes.seqid),
+    output:
+        ofile = ws_path("coloc/master_coloc.txt"),
+    params:
+        outdir = config.get("workspace_path")
+    log:
+        ws_path("logs/coloc/master_file.log"),
+    resources:
+        runtime=lambda wc, attempt: 999 + attempt * 60,
+    shell:
+        """
+        cat {params.outdir}/cojo/{seqid}/finemaping/*_coloc_info_table.tsv >> {output.ofile}
+        """
+