Merge pull request #86 from acidgenomics/master

v0.4.4
hbc · Sep 9, 2019 · 6516543 · 6516543
2 parents 5a22277 + 13b1b1e
commit 6516543
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: bcbioSingleCell
 Title: bcbio Single-Cell RNA-Seq
 Description: R package for bcbio single-cell RNA-seq analysis.
-Version: 0.4.3
-Date: 2018-08-27
+Version: 0.4.4
+Date: 2018-09-09
 Authors@R: c(
     person(
         given = "Michael",
@@ -54,12 +54,12 @@ LazyData: false
 Depends:
     R (>= 3.6),
     SingleCellExperiment (>= 1.6),
-    basejump (>= 0.11.11)
+    basejump (>= 0.11.14)
 Imports:
     acidplots (>= 0.2.14),
     bcbioBase (>= 0.6.10),
-    bioverbs (>= 0.2.7),
-    goalie (>= 0.3.6),
+    bioverbs (>= 0.2.9),
+    goalie (>= 0.3.7),
     BiocGenerics (>= 0.30),
     BiocParallel (>= 1.18),
     IRanges (>= 2.18.2),
@@ -73,7 +73,7 @@ Imports:
     methods,
     utils
 Suggests:
-    acidroxygen (>= 0.1),
+    acidroxygen (>= 0.1.2),
     BiocStyle (>= 2.12),
     R.utils (>= 2.9),
     knitr (>= 1.24),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+## bcbioSingleCell 0.4.4 (2019-09-09)
+
+### Minor changes
+
+- `bcbioSingleCell`: Internal generator now calls `importSampleData` using
+  `pipeline = "bcbio"` argument, so we don't run into breaking changes when
+  handling user metadata in a future basejump update.
+- Updated basejump dependency versions.
+
 ## bcbioSingleCell 0.4.3 (2019-08-27)
 
 ### Minor changes

diff --git a/R/AllGenerators.R b/R/AllGenerators.R
@@ -137,7 +137,11 @@ bcbioSingleCell <- function(
     allSamples <- TRUE
     sampleData <- NULL
     if (isString(sampleMetadataFile)) {
-        sampleData <- importSampleData(sampleMetadataFile, lanes = lanes)
+        sampleData <- importSampleData(
+            file = sampleMetadataFile,
+            lanes = lanes,
+            pipeline = "bcbio"
+        )
         ## Error on incorrect reverse complement input.
         if ("sequence" %in% colnames(sampleData)) {
             sampleDirSequence <- str_extract(names(sampleDirs), "[ACGT]+$")

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/authors.html b/docs/authors.html