feat: expose summary statistics qc and locus breaker steps to hydra cli (#716)

project-defiant · Szymon Szyszkowski · web-flow · commit ea80fbfb5662 · 2024-07-25T11:26:50.000+01:00
* feat: expose summary statistics qc to hydra cli

* feat: expose locus breaker clumping step

---------

Co-authored-by: Szymon Szyszkowski &lt;ss60@mib117351s.internal.sanger.ac.uk&gt;
diff --git a/docs/python_api/steps/locus_breaker_clumping.md b/docs/python_api/steps/locus_breaker_clumping.md
@@ -0,0 +1,5 @@
+---
+title: locus_breaker_clumping
+---
+
+::: gentropy.locus_breaker_clumping.LocusBreakerClumpingStep
diff --git a/docs/python_api/steps/summary_statistics_qc.md b/docs/python_api/steps/summary_statistics_qc.md
@@ -0,0 +1,5 @@
+---
+title: summary_statistics_qc
+---
+
+::: gentropy.sumstat_qc_step.SummaryStatisticsQCStep
diff --git a/src/gentropy/config.py b/src/gentropy/config.py
@@ -532,3 +532,7 @@ def register_config() -> None:
         group="step", name="window_based_clumping", node=WindowBasedClumpingStepConfig
     )
     cs.store(group="step", name="susie_finemapping", node=FinemapperConfig)
+    cs.store(group="step", name="summary_statistics_qc", node=GWASQCStep)
+    cs.store(
+        group="step", name="locus_breaker_clumping", node=LocusBreakerClumpingConfig
+    )

-Original file line number
+Diff line change
@@ @@ -0,0 +1,5 @@ @@
 +---
 +title: locus_breaker_clumping
 +---
++
 +::: gentropy.locus_breaker_clumping.LocusBreakerClumpingStep
Original file line number	Diff line number	Diff line change
`@@ -532,3 +532,7 @@ def register_config() -> None:`
`532`	`532`	`group="step", name="window_based_clumping", node=WindowBasedClumpingStepConfig`
`533`	`533`	`)`
`534`	`534`	`cs.store(group="step", name="susie_finemapping", node=FinemapperConfig)`
	`535`	`+ cs.store(group="step", name="summary_statistics_qc", node=GWASQCStep)`
	`536`	`+ cs.store(`
	`537`	`+ group="step", name="locus_breaker_clumping", node=LocusBreakerClumpingConfig`
	`538`	`+ )`