add rule

workflow/rules/summarize.smk

@@ -0,0 +1,47 @@
+rule summarize_sumstats:
+    input:
+        ws_path("pickle/{seqid}.pkl"),
+    output:
+        temp(ws_path("if/{seqid}.if.txt")),
+        temp(ws_path("min_P/{seqid}.nlargest.txt")),
+        ws_path("plots/{seqid}.png"),
+    conda:
+        "../scripts/gwaspipe/environment.yml"
+    params:
+        format=config.get("params").get("summarize_sumstats").get("input_format"),
+        config_file=config.get("params").get("summarize_sumstats").get("config_file"),
+        output_path=config.get("workspace_path"),
+    resources:
+        runtime=lambda wc, attempt: attempt * 60,
+    shell:
+        "python workflow/scripts/gwaspipe/src/gwaspipe.py "
+        "-f {params.format} "
+        "-c {params.config_file} "
+        "-i {input} "
+        "-o {params.output_path}"
+
+
+rule create_if_table:
+    input:
+        expand(ws_path("if/{seqid}.if.txt"), seqid=analytes.seqid),
+    output:
+        ws_path("inflation_factors_table.tsv"),
+    conda:
+        "../envs/create_report_table.yaml"
+    params:
+        input_path=ws_path("if"),
+    shell:
+        "python workflow/scripts/create_report_table.py -i {params.input_path} -o {output}"
+
+
+rule create_min_pvalue_table:
+    input:
+        expand(ws_path("min_P/{seqid}.nlargest.txt"), seqid=analytes.seqid),
+    output:
+        ws_path("min_pvalue_table.tsv"),
+    conda:
+        "../envs/create_report_table.yaml"
+    params:
+        input_path=ws_path("min_P"),
+    shell:
+        "python workflow/scripts/create_report_table.py -i {params.input_path} -o {output}"