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birneylab · Dec 10, 2024 · e603df1 · e603df1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,16 +1,10 @@
-# nf-core/stitchimpute: Changelog
+# birneylab/flexlmm: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [July 14th 2023]
+## v2.0.0 - [December 10th 2024]
 
-Initial release of birneylab/stitchimpute, created with the [nf-core](https://nf-co.re/) template and stripped of the references to it being an official nf-core pipeline.
-
-### `Added`
-
-### `Fixed`
-
-### `Dependencies`
-
-### `Deprecated`
+Major change and simplification in workflow logic with the aim of facilitating future integration of an eQTL branch.
+Change of the permutation approach to be performed on the residuals instead than on the genotypes.
+Deprecation of the `permute_by` parameter as grouped permutation are not possible on the low-dimensional projection of the residuals.
diff --git a/modules/local/r/aireml.nf b/modules/local/r/aireml.nf
@@ -36,7 +36,7 @@ process AIREML {
 
     y <- y[!is.na(y)]
 
-    samples <- intersect(samples_K, names(y))
+    samples <- intersect(intersect(samples_K, names(y)), rownames(X))
     X <- X[match(samples, rownames(X)), , drop = FALSE]
     y <- y[match(samples, names(y))]
     K <- K[match(samples, rownames(K)), match(samples, colnames(K))]

diff --git a/nextflow.config b/nextflow.config
@@ -258,7 +258,7 @@ manifest {
     description     = "Flexible linear mixed model framework for Genome Wide Association Studies"
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0.6'
+    version = '2.0.0'
     doi             = ''
 }