turns back on somalier relatedness

ManavalanG · ManavalanG · commit c591564ee3c7 · 2025-05-04T20:32:34.000-05:00
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -41,8 +41,8 @@ if not EXOME_MODE:
 rule all:
     input:
         ##### ancestry and relatedness #####
-        # # somalier
-        # OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",
+        # somalier
+        OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",
         # OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.html",
         ##### coverage #####
         # samtools
diff --git a/workflow/rules/aggregate_results.smk b/workflow/rules/aggregate_results.smk
@@ -189,7 +189,7 @@ rule multiqc_aggregation_all_samples:
         [get_priorQC_filepaths(sample, SAMPLES_CONFIG) for sample in SAMPLES_CONFIG.keys()] if INCLUDE_PRIOR_QC_DATA else [],
         expand(
             [
-                # OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",
+                OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",
                 # OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.html",
                 OUT_DIR / "{sample}" / "qc" / "samtools-stats" / "{sample}.txt",
                 OUT_DIR / "{sample}" / "qc" / "qualimap" / "{sample}" / "qualimapReport.html",

Original file line number	Diff line number	Diff line change
`@@ -189,7 +189,7 @@ rule multiqc_aggregation_all_samples:`
`189`	`189`	`[get_priorQC_filepaths(sample, SAMPLES_CONFIG) for sample in SAMPLES_CONFIG.keys()] if INCLUDE_PRIOR_QC_DATA else [],`
`190`	`190`	`expand(`
`191`	`191`	`[`
`192`		`- # OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",`
	`192`	`+ OUT_DIR / "project_level_qc" / "somalier" / "relatedness" / "somalier.html",`
`193`	`193`	`# OUT_DIR / "project_level_qc" / "somalier" / "ancestry" / "somalier.somalier-ancestry.html",`
`194`	`194`	`OUT_DIR / "{sample}" / "qc" / "samtools-stats" / "{sample}.txt",`
`195`	`195`	`OUT_DIR / "{sample}" / "qc" / "qualimap" / "{sample}" / "qualimapReport.html",`