Modified graphrra.nf for Apptainer/Singularity.

nf-core · Nov 7, 2024 · 84a919a · 84a919a
1 parent 9f0de4f
commit 84a919a
Showing 1 changed file with 1 addition and 8 deletions.
diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf
@@ -27,14 +27,7 @@ process MAGECK_GRAPHRRA {
     #### Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text.
     ####
     #### Orient a reference sequence according to reads orientation.
-    library(BiocFileCache)
-    bfc <- BiocFileCache("~/.cache/R/ExperimentHub")
-    library(ExperimentHub)
-    res <- bfcquery(bfc, "experimenthub.index.rds", field="rname", exact=TRUE)
-    bfcremove(bfc, rids=res\$rid)
-    eh = ExperimentHub()
-    Sys.setenv(BIOMART_CACHE=tempdir())
-
+    Sys.setenv(HOME = getwd())  # Required for Singularity/Apptainer
     library(MAGeCKFlute)
     library(ggplot2)
     options(ggrepel.max.overlaps = Inf)